bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrio choleraePhage K139: Complete Genome Sequence and Comparative Genomics of Related Phages
Authors: Kapfhammer Dagmar , Blass Julia , Evers Stefan , Reidl Joachim 
Published: November 2002

ABSTRACTIn this report, we characterize the complete genome sequence of the temperate phage K139, which morphologically belongs to theMyoviridaephage family (P2 and 186). The prophage genome consists of 33,106 bp, and the overall GC content is 48.9%. Forty-four open reading frames were identified. Homology analysis and motif search were used to assign possible functions for the genes, revealing a close relationship to P2-like phages. By Southern blot screening of aVibrio choleraestrain collection, two highly K139-related phage sequences were detected in non-O1, non-O139 strains. Combinatorial PCR analysis revealed almost identical genome organizations. One region of variable gene content was identified and sequenced. Additionally, the tail fiber genes were analyzed, leading to the identification of putative host-specific sequence variations. Furthermore, a K139-encoded Dam methyltransferase was characterized.
Arginine Operator Binding by Heterologous and Chimeric ArgR Repressors fromEscherichia coliandBacillus stearothermophilus
Authors: Ghochikyan Anahit , Karaivanova Iovka Miltcheva , Lecocq Michèle , Vusio Patricia , Arnaud Marie-Claire , Snapyan Marina , Weigel Pierre , Guével Laetitia , Buckle Malcolm , Sakanyan Vehary 
Published: November 2002

ABSTRACTBacillus stearothermophilusArgR binds efficiently to theEscherichia coli carABoperator, whereas theE. colirepressor binds very poorly to theargCooperator ofB. stearothermophilus. In order to elucidate this contradictory behavior between ArgRs, we constructed chimeric proteins by swapping N-terminal DNA-binding and C-terminal oligomerization domains or by exchanging the linker peptide. Chimeras carrying theE. coliDNA-binding domain and theB. stearothermophilusoligomerization domain showed sequence-nonspecific rather than sequence-specific interactions withargoperators. Chimeras carrying theB. stearothermophilusDNA-binding domain andE. colioligomerization domain exhibited a high DNA-binding affinity for theB. stearothermophilus argCoandE. coli carABoperators and repressed the reporter-gene transcription from theB. stearothermophilusPargCocontrol region in vitro; arginine had no effect on, and indeed even decreased, their DNA-binding affinity. With the protein array method, we showed that the wild-typeB. stearothermophilusArgR and derivatives of it containing only the exchanged linker fromE. coliArgR or carrying theB. stearothermophilusDNA-binding domain along with the linker and the α4 regions were able to bindargCocontaining the single Arg box. This binding was weaker than binding to the two-box operator but was no longer arginine dependent. Several lines of observations indicate that the α4 helix in the oligomerization domain and the linker peptide can contribute to the recognition of single or double Arg boxes and therefore to the operator DNA-binding specificity in similar but not identical ArgR repressors from two distant bacteria.
Regulation of the Hydrogenase-4 Operon of
Escherichia coli
by the σ
54
-Dependent Transcriptional Activators FhlA and HyfR
Authors: Skibinski David A. G. , Golby Paul , Chang Yung-Sheng , Sargent Frank , Hoffman Ralf , Harper R. , Guest John R. , Attwood Margaret M. , Berks Ben C. , Andrews Simon C. 
Published: November 2002

ABSTRACT

The
hyf
locus (
hyfABCDEFGHIJ-hyfR-focB
) of
Escherichia coli
encodes a putative 10-subunit hydrogenase complex (hydrogenase-4 [Hyf]); a potential σ
54
-dependent transcriptional activator, HyfR (related to FhlA); and a putative formate transporter, FocB (related to FocA). In order to gain insight into the physiological role of the Hyf system, we investigated
hyf
expression by using a
hyfA-lacZ
transcriptional fusion. This work revealed that
hyf
is induced under fermentative conditions by formate at a low pH and in an FhlA-dependent fashion. Expression was σ
54
dependent and was inhibited by HycA, the negative transcriptional regulator of the formate regulon. Thus,
hyf
expression resembles that of the
hyc
operon. Primer extension analysis identified a transcriptional start site 30 bp upstream of the
hyfA
structural gene, with appropriately located −24 and −12 boxes indicative of a σ
54
-dependent promoter. No reverse transcriptase PCR product could be detected for
hyfJ-hyfR
, suggesting that
hyfR-focB
may be independently transcribed from the rest of the
hyf
operon. Expression of
hyf
was strongly induced (∼1,000-fold) in the presence of a multicopy plasmid expressing
hyfR
from a heterologous promoter. This induction was dependent on low pH, anaerobiosis, and postexponential growth and was weakly enhanced by formate. The
hyfR-
expressing plasmid increased
fdhF-lacZ
transcription just twofold but did not influence the expression of
hycB-lacZ
. Interestingly, inactivation of the chromosomal
hyfR
gene had no effect on
hyfA-lacZ
expression. Purified HyfR was found to specifically interact with the
hyf
promoter/operator region. Inactivation of the
hyf
operon had no discernible effect on growth under the range of conditions tested. No Hyf-derived hydrogenase or formate dehydrogenase activity could be detected, and no Ni-containing protein corresponding to HyfG was observed.
Differential Expression of the CO
2
Fixation Operons of
Rhodobacter sphaeroides
by the Prr/Reg Two-Component System during Chemoautotrophic Growth
Authors: Gibson Janet L. , Dubbs James M. , Tabita F. Robert 
Published: November 2002

ABSTRACT

In
Rhodobacter sphaeroides
, the two
cbb
operons encoding duplicated Calvin-Benson Bassham (CBB) CO
2
fixation reductive pentose phosphate cycle structural genes are differentially controlled. In attempts to define the molecular basis for the differential regulation, the effects of mutations in genes encoding a subunit of Cbb3 cytochrome oxidase,
ccoP,
and a global response regulator,
prrA
(
regA
), were characterized with respect to CO
2
fixation (
cbb
) gene expression by using translational
lac
fusions to the
R. sphaeroides
cbb

I

and

cbb
II

promoters. Inactivation of the
ccoP
gene resulted in derepression of both promoters during chemoheterotophic growth, where
cbb
expression is normally repressed; expression was also enhanced over normal levels during phototrophic growth. The
prrA
mutation effected reduced expression of

cbb
I

and

cbb
II

promoters during chemoheterotrophic growth, whereas intermediate levels of expression were observed in a double
ccoP prrA
mutant.
PrrA
and
ccoP1 prrA
strains cannot grow phototrophically, so it is impossible to examine
cbb
expression in these backgrounds under this growth mode. In this study, however, we found that PrrA mutants of
R. sphaeroides
were capable of chemoautotrophic growth, allowing, for the first time, an opportunity to directly examine the requirement of PrrA for
cbb
gene expression in vivo under growth conditions where the CBB cycle and CO
2
fixation are required. Expression from the

cbb
II

promoter was severely reduced in the PrrA mutants during chemoautotrophic growth, whereas

cbb
I

expression was either unaffected or enhanced. Mutations in
ccoQ
had no effect on expression from either promoter. These observations suggest that the Prr signal transduction pathway is not always directly linked to Cbb3 cytochrome oxidase activity, at least with respect to
cbb
gene expression. In addition,
lac
fusions containing various lengths of the

cbb
I

promoter demonstrated distinct sequences involved in positive regulation during photoautotrophic versus chemoautotrophic growth, suggesting that different regulatory proteins may be involved. In
Rhodobacter capsulatus
, ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) expression was not affected by
cco
mutations during photoheterotrophic growth, suggesting that differences exist in signal transduction pathways regulating
cbb
genes in the related organisms.
Gene Islands Integrated into tRNA
Gly
Genes Confer Genome Diversity on a
Pseudomonas aeruginosa
Clone
Authors: Larbig Karen D. , Christmann Andreas , Johann André , Klockgether Jens , Hartsch Thomas , Merkl Rainer , Wiehlmann Lutz , Fritz Hans-Joachim , Tümmler Burkhard 
Published: November 2002

ABSTRACT

Intraclonal genome diversity of
Pseudomonas aeruginosa
was studied in one of the most diverse mosaic regions of the
P. aeruginosa
chromosome. The ca. 110-kb large hypervariable region located near the
lipH
gene in two members of the predominant
P. aeruginosa
clone C, strain C and strain SG17M, was sequenced. In both strains the region consists of an individual strain-specific gene island of 111 (strain C) or 106 (SG17M) open reading frames (ORFs) and of a 7-kb stretch of clone C-specific sequence of 9 ORFs. The gene islands are integrated into conserved tRNA
Gly
genes and have a bipartite structure. The first part adjacent to the tRNA gene consists of strain-specific ORFs encoding metabolic functions and transporters, the majority of which have homologs of known function in other eubacteria, such as hemophores, cytochrome
c
biosynthesis, or mercury resistance. The second part is made up mostly of ORFs of yet-unknown function. Forty-seven of these ORFs are mutual homologs with a pairwise amino acid sequence identity of 35 to 88% and are arranged in the same order in the two gene islands. We hypothesize that this novel type of gene island derives from mobile elements which, upon integration, endow the recipient with strain-specific metabolic properties, thus possibly conferring on it a selective advantage in its specific habitat.
A
Sinorhizobium meliloti
Lipopolysaccharide Mutant Altered in Cell Surface Sulfation
Authors: Keating David H. , Willits Michael G. , Long Sharon R. 
Published: November 2002

ABSTRACT

The
Rhizobium
-legume symbiosis involves the formation of a novel plant organ, the nodule, in which intracellular bacteria reduce molecular dinitrogen in exchange for plant photosynthates. Nodule development requires a bacterial signal referred to as Nod factor, which in
Sinorhizobium meliloti
is a β-(1,4)-linked tetramer of
N
-acetylglucosamine containing
N
-acyl and
O
-acetyl modifications at the nonreducing end and a critical 6-
O
-sulfate at the reducing end. This sulfate modification requires the action of three gene products:
nodH
, which catalyzes the sulfonyl transfer, and
nodPQ
, which produce the activated form of sulfate, 3′-phosphoadenosine-5′-phosphosulfate. It was previously reported that
S. meliloti
cell surface polysaccharides are also covalently modified by sulfate in a reaction dependent on NodPQ. We have further characterized this unique form of bacterial carbohydrate modification. Our studies have determined that one of the
nodPQ
mutant strains used in the initial study of sulfation of cell surface harbored a second unlinked mutation. We cloned the gene affected by this mutation (referred to as
lps-212
) and found it to be an allele of
lpsL
, a gene previously predicted to encode a UDP-glucuronic acid epimerase. We demonstrated that
lpsL
encoded a UDP-glucuronic acid epimerase activity that was reduced in the
lps-212
mutant. The
lps-212
mutation resulted in an altered lipopolysaccharide structure that was reduced in sulfate modification in vitro and in vivo. Finally, we determined that the
lps-212
mutation resulted in a reduced ability to elicit the formation of plant nodules and by altered infection thread structures that aborted prematurely.
Evolution of the C
30
Carotenoid Synthase CrtM for Function in a C
40
Pathway
Authors: Umeno Daisuke , Tobias Alexander V. , Arnold Frances H. 
Published: November 2002

ABSTRACT

The C
30
carotene synthase CrtM from
Staphylococcus aureus
and the C
40
carotene synthase CrtB from
Erwinia uredovora
were swapped into their respective foreign C
40
and C
30
biosynthetic pathways (heterologously expressed in
Escherichia coli
) and evaluated for function. Each displayed negligible ability to synthesize the natural carotenoid product of the other. After one round of mutagenesis and screening, we isolated 116 variants of CrtM able to synthesize C
40
carotenoids. In contrast, we failed to find a single variant of CrtB with detectable C
30
activity. Subsequent analysis revealed that the best CrtM mutants performed comparably to CrtB in an in vivo C
40
pathway. These mutants showed significant variation in performance in their original C
30
pathway, indicating the emergence of enzymes with broadened substrate specificity as well as those with shifted specificity. We discovered that Phe 26 alone determines the specificity of CrtM. The plasticity of CrtM with respect to its substrate and product range highlights the potential for creating further new carotenoid backbone structures.
Identification by RNA Profiling and Mutational Analysis of the Novel Copper Resistance Determinants CrdA (HP1326), CrdB (HP1327), and CzcB (HP1328) in
Helicobacter pylori
Authors: Waidner Barbara , Melchers Klaus , Ivanov Igor , Loferer Hannes , Bensch Klaus W. , Kist Manfred , Bereswill Stefan 
Published: November 2002

ABSTRACT

Mechanisms involved in maintaining cytoplasmic metal ion homeostasis play a central role in the adaptation of
Helicobacter pylori
to the changing gastric environment. An investigation of the global regulatory responses to copper ions by using RNA profiling with a threshold factor of 4.0 revealed that copper induces transcription of 19
H. pylori
genes and that only the ferritin gene
pfr
is repressed. The 57-fold copper induction identified the HP1326 gene encoding an
H. pylori
-specific protein as a candidate for a novel copper resistance determinant. The HP1326 gene is expressed as a monocistronic unit, and two small HP1326 mRNAs are copper induced. The HP1326 protein is secreted and is required for copper resistance maintained by cytoplasmic copper homeostasis, as
H. pylori
HP1326 mutants were copper sensitive and displayed increased copper induction of HP1326 transcription as well as elevated copper repression of ferritin synthesis. The clear copper-sensitive phenotype displayed by
H. pylori
HP1327 and HP1328 mutants provides strong evidence that the HP1326 protein, together with the signal peptide site of the
H. pylori
-specific protein HP1327, whose gene is located downstream from that encoding HP1326, and the CzcB and CzcA metal efflux system component homologs HP1328 and HP1329, constitutes a novel type of copper efflux pump, as discussed below. The HP1329 gene could not be inactivated, but the 14-fold transcriptional copper induction determined by RNA profiling points towards a function of the encoded CzcA homolog in copper resistance. In summary, results from RNA profiling identified the novel
H. pylori
-specific copper resistance determinants CrdA (HP1326) and CrdB (HP1327), which are required for adaptation to copper-rich environmental conditions.
Isolation of Glucocardiolipins from
Geobacillus stearothermophilus
NRS 2004/3a
Authors: Schäffer Christina , Beckedorf Anke I. , Scheberl Andrea , Zayni Sonja , Peter-Katalinić Jasna , Messner Paul 
Published: November 2002

ABSTRACT

Glucose-substituted cardiolipins account for about 4 mol% of total phospholipid extracted from exponentially grown cells of
Geobacillus stearothermophilus
NRS 2004/3a. Individual glucocardiolipin species exhibited differences in fatty acid substitution, with iso-C
15:0
and anteiso-C
17:0
prevailing. The compounds were purified to homogeneity by a novel protocol and precharacterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
Up-Regulated Expression of the

cbb
I

and

cbb
II

Operons during Photoheterotrophic Growth of a Ribulose 1,5-Bisphosphate Carboxylase-Oxygenase Deletion Mutant of
Rhodobacter sphaeroides
Authors: Smith Stephanie A. , Tabita F. Robert 
Published: November 2002

ABSTRACT

In a
Rhodobacter sphaeroides
ribulose 1,5-bisphosphate carboxylase-oxygenase deletion strain that requires an exogenous electron donor for photoheterotrophic growth, transcription of the genes of the Calvin-Benson-Bassham (CBB) cycle was increased. This finding pointed to a potential physiological effector that enhances the capability of the positive transcriptional activator CbbR to mediate
cbb
transcription. This effector is most likely ribulose 1,5-bisphosphate or a metabolite derived from this CBB pathway intermediate.
DNA Microarray Analysis of the Expression Profile of
Escherichia coli
in Response to Treatment with 4,5-Dihydroxy-2-Cyclopenten-1-One
Authors: Phadtare Sangita , Kato Ikunoshin , Inouye Masayori 
Published: November 2002

ABSTRACT

We carried out DNA microarray-based global transcript profiling of
Escherichia coli
in response to 4,5-dihydroxy-2-cyclopenten-1-one to explore the manifestation of its antibacterial activity. We show that it has widespread effects in
E. coli
affecting genes encoding proteins involved in cell metabolism and membrane synthesis and functions. Genes belonging to the regulon involved in synthesis of Cys are upregulated. In addition,
rpoS
and RpoS-regulated genes responding to various stresses and a number of genes responding to oxidative stress are upregulated.
Low-Temperature-Induced Changes in Composition and Fluidity of Lipopolysaccharides in the Antarctic Psychrotrophic BacteriumPseudomonas syringae
Authors: Kumar G. Seshu , Jagannadham M. V. , Ray M. K. 
Published: November 2002

ABSTRACTThe Antarctic psychrotrophic bacteriumPseudomonas syringaewas more sensitive to polymyxin B at a lower (4°C) temperature of growth than at a higher (22°C) temperature. The amount of hydroxy fatty acids in the lipopolysaccharides (LPS) also increased at the lower temperature. These changes correlated with the increase in fluidity of the hydrophobic phase of lipopolysaccharide aggregates in vitro.
ATP-Binding Cassette Transporter 1 Participates in LDL Oxidation by Artery Wall Cells
Authors: Reddy Srinivasa T. , Hama Susan , Ng Carey , Grijalva Victor , Navab Mohamad , Fogelman Alan M. 
Published: November 2002

Objective—We have previously reported that products of the lipoxygenase pathway, hydroperoxyoctadecadienoic acid and hydroperoxyeicosatetraenoic acid, as well as cholesterol linoleate hydroperoxides, collectively termed seeding molecules, are removed by apolipoprotein A-I (apoA-I) from the artery wall cells and render low density lipoprotein (LDL) resistant to oxidation by human artery wall cells. The mechanisms by which oxidized lipids are transported and/or transferred to lipoproteins and the pathways by which apoA-I facilitates their removal remain unclear. ATP-binding cassette transporter 1 (ABCA1) is known to facilitate the release of cellular phospholipids and cholesterol from the plasma membrane to apoA-I and high density lipoprotein. Therefore, we evaluated whether ABCA1 participates in LDL oxidation.Methods and Results—In this report, we show that (1) chemical inhibitors of ABCA1 function, glyburide and DIDS, block artery wall cell–mediated oxidative modification of LDL, (2) inhibition of ABCA1 with the use of antisense (but not sense) oligonucleotides prevents LDL-induced lipid hydroperoxide formation and LDL-induced monocyte chemotactic activity by the artery wall cells, and (3) oxysterols that induce ABCA1 expression, such as 22(R)hydroxycholesterol, enhance cell-mediated LDL oxidation. Furthermore, we also show that 22(R)hydroxycholesterol induces the production of reactive oxygen species in the artery wall cells, which can be removed by incubating the artery wall cells with apoA-I.Conclusions—Our data suggest that ABCA1 plays an important role in artery wall cell–mediated modification/oxidation of LDL by modulating the release of reactive oxygen species from artery wall cells that are necessary for LDL oxidation.
Endothelial Determinants of Dendritic Cell Adhesion and Migration
Authors: Weis Michael , Schlichting Christoph L. , Engleman Edgar G. , Cooke John P. 
Published: November 2002

Objective—Atherosclerosis is a chronic disease triggered by endothelial injury and sustained by inflammation. Dendritic cells (DCs) are critical for the cell-mediated arm of an immune response and are known to influence inflammatory immunity. A fundamental aspect of DC function is their capacity to adhere and migrate through vascular endothelial cells (ECs). We investigated the role of endothelial activation and dysregulation of the NO pathway on DC adhesion and migration.Methods and Results—We discovered that DC adhesion and migration are modulated by changes in endothelial function. DC adhesion and transmigration were markedly increased after exposing ECs to hypoxia, oxidized low density lipoprotein, or tumor necrosis factor-α. Specifically, inhibition of endothelial NO synthase increased DC binding and transmigration.l-Arginine or 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibition partially decreased DC-EC interaction.Conclusions—The results of this study suggest that the adhesion and migration of DCs are increased by stimuli known to accelerate atherogenesis. Vice versa, augmentation of endothelial NO synthase activity prevents DC adhesion. These findings may provide insight into the inflammatory processes occurring in atherosclerosis. Because DCs control immunity, regulating DC-EC interaction may be relevant to inflammation and atherogenesis.
Pharmacological Potentiation of Natriuretic Peptide Limits Polymorphonuclear Neutrophil-Vascular Cell Interactions
Authors: Mtairag El Mostafa , Houard Xavier , Rais Samira , Pasquier Catherine , Oudghiri Mounia , Jacob Marie-Paule , Meilhac Olivier , Michel Jean-Baptiste 
Published: November 2002

Objective—Activated polymorphonuclear neutrophils (PMNs) are the main source of circulating neutral endopeptidase (NEP). We tested the hypothesis that NEP inhibition could potentiate the effect of atrial natriuretic peptide (ANP) on PMN-vascular cell interactions in vitro.Methods and Results—ANP alone and its potentiation by retrothiorphan, the NEP inhibitor, significantly inhibited superoxide, lysozyme, and matrix metalloproteinase (MMP)-9 release byN-formyl-Met-Leu-Phe-stimulated PMNs. Activated PMNs degraded exogenous ANP, which was prevented by NEP inhibition. Hypoxia significantly increased the adhesion of PMNs to endothelial cells and their subsequent MMP-9 release by 60% and 150%, respectively (P<0.01). ANP and its potentiation by retrothiorphan limited PMN adhesion to hypoxic endothelial cells and thus decreased their MMP-9 release (P<0.01). Smooth muscle cells (SMCs) incubated with conditioned medium ofN-formyl-Met-Leu-Phe-stimulated PMNs exhibited morphological and biochemical changes characteristic of apoptosis (terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling positivity, nuclear condensation/fragmentation, poly ADP-ribose polymerase cleavage, and DNA laddering). SMC detachment and subsequent apoptosis could be related to leukocyte elastase-induced pericellular proteolysis, inasmuch as both events are inhibited by elastase inhibitors. ANP and its potentiation by retrothiorphan were able to limit elastase release, fibronectin degradation, and SMC apoptosis.Conclusions—ANP potentiation by NEP inhibition could limit PMN activation and its consequences on vascular cells.
PERVERSION OF POWER: WITCHCRAFT AND THE SEXUALITY OF EVIL IN THE SOUTH AFRICAN LOWVELD
Authors: Niehaus Isak 
Published: November 2002

AbstractDuring recent years, fears of witchcraft and the violent punishment of witches have become commonplace in the Bushbuckridge region of the South African lowveld. My fieldwork in a village of Bushbuckridge highlights the crucial importance of sexuality in witchcraft discourses. Narratives about the sexual practices of witches formed part of the same moral system as those about the unacceptable sexual conduct of ordinary villagers. But there were also important differences between these. Whilst the unacceptable sexual conduct of ordinary villagers transgressed general moral ideals, the sexual practices of witches transgressed local hierarchies of domination and were conceptualised as perversions of power. I suggest that the most appropriate perspective on witchcraft is one that seeks to integrate a concern with broader political economic processes with a rigorous analysis of the micro-politics of sexuality, kinship and morality.