bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of the CopB Auxiliary Replication Control System on Stability of Maintenance of Par
+
Plasmid R1
Authors: Olsson Jan A. , Paulsson Johan , Nordström Kurt 
Published: December 2003

ABSTRACT

Plasmid R1 is a low-copy-number plasmid that is present at a level of about four or five copies per average cell. The copy number is controlled posttranscriptionally at the level of synthesis of the rate-limiting initiator protein RepA. In addition to this, R1 has an auxiliary system that derepresses a second promoter at low copy numbers, leading to increased
repA
mRNA synthesis. This promoter is normally switched off by a constitutively synthesized plasmid-encoded repressor protein, CopB; in cells with low copy numbers, the concentration of CopB is low and the promoter is derepressed. Here we show that the rate of loss of a Par
+
derivative of the basic replicon of R1 increased about sevenfold when the cells contained a high concentration of the CopB protein formed from a compatible plasmid.
Characterization of the 101-Kilobase-Pair Megaplasmid pKB1, Isolated from the Rubber-Degrading BacteriumGordonia westfalicaKb1
Authors: Bröker Daniel , Arenskötter Matthias , Legatzki Antje , Nies Dietrich H. , Steinbüchel Alexander 
Published: December 2003

ABSTRACTThe complete sequence of the circular 101,016-bp megaplasmid pKB1 from thecis-1,4-polyisoprene-degrading bacteriumGordonia westfalicaKb1, which represents the first described extrachromosomal DNA of a member of this genus, was determined. Plasmid pKB1 harbors 105 open reading frames. The predicted products of 46 of these are significantly related to proteins of known function. Plasmid pKB1 is organized into three functional regions that are flanked by insertion sequence (IS) elements: (i) a replication and putative partitioning region, (ii) a putative metabolic region, and (iii) a large putative conjugative transfer region, which is interrupted by an additional IS element. Southern hybridization experiments revealed the presence of another copy of this conjugational transfer region on the bacterial chromosome. The origin of replication (oriV) of pKB1 was identified and used for construction ofEscherichia coli-Gordoniashuttle vectors, which was also suitable for several otherGordoniaspecies and related genera. The metabolic region included the heavy-metal resistance genecadA, encoding a P-type ATPase. Expression ofcadAinE. colimediated resistance to cadmium, but not to zinc, and decreased the cellular content of cadmium in this host. WhenG. westfalicastrain Kb1 was cured of plasmid pKB1, the resulting derivative strains exhibited slightly decreased cadmium resistance. Furthermore, they had lost the ability to use isoprene rubber as a sole source of carbon and energy, suggesting that genes essential for rubber degradation are encoded by pKB1.
Multiple Formate Dehydrogenase Enzymes in the Facultative Methylotroph
Methylobacterium extorquens
AM1 Are Dispensable for Growth on Methanol
Authors: Chistoserdova Ludmila , Laukel Markus , Portais Jean-Charles , Vorholt Julia A. , Lidstrom Mary E. 
Published: December 2003

ABSTRACT

Formate dehydrogenase has traditionally been assumed to play an essential role in energy generation during growth on C
1
compounds. However, this assumption has not yet been experimentally tested in methylotrophic bacteria. In this study, a whole-genome analysis approach was used to identify three different formate dehydrogenase systems in the facultative methylotroph
Methylobacterium extorquens
AM1 whose expression is affected by either molybdenum or tungsten. A complete set of single, double, and triple mutants was generated, and their phenotypes were analyzed. The growth phenotypes of the mutants suggest that any one of the three formate dehydrogenases is sufficient to sustain growth of
M. extorquens
AM1 on formate, while surprisingly, none is required for growth on methanol or methylamine. Nuclear magnetic resonance analysis of the fate of [
13
C]methanol revealed that while cells of wild-type
M. extorquens
AM1 as well as cells of all the single and the double mutants continuously produced [
13
C]bicarbonate and
13
CO
2
, cells of the triple mutant accumulated [
13
C]formate instead. Further studies of the triple mutant showed that formate was not produced quantitatively and was consumed later in growth. These results demonstrated that all three formate dehydrogenase systems must be inactivated in order to disrupt the formate-oxidizing capacity of the organism but that an alternative formate-consuming capacity exists in the triple mutant.
Null Mutation of HvrA Compensates for Loss of an Essential
relA/spoT
-Like Gene in
Rhodobacter capsulatus
Authors: Masuda Shinji , Bauer Carl E. 
Published: December 2003

ABSTRACT

We report that a single
relA/spoT
-like gene exists on the
Rhodobacter capsulatus
chromosome, and its mutational loss is lethal. This gene could be mutated only under a mutational background of a null mutation in the nucleoid protein HvrA. This result suggests that there may be a direct link between HvrA-regulated promoters and the ppGpp-related stringent response.
Transcriptome Analysis of the Response of
Pseudomonas aeruginosa
to Hydrogen Peroxide
Authors: Palma Marco , DeLuca Darrow , Worgall Stefan , Quadri Luis E. N. 
Published: December 2003

ABSTRACT

Pseudomonas aeruginosa
must often overcome a high concentration of oxidants to successfully infect the human host. We report here the results of a transcriptome profiling comparing cells treated with H
2
O
2
and untreated controls. The data indicate that the early response of
P. aeruginosa
to H
2
O
2
consists of an upregulation of protective mechanisms and a downregulation of primary metabolism.
Production of Heterologous and Chimeric Scaffoldins by
Clostridium acetobutylicum
ATCC 824
Authors: Perret S. , Casalot L. , Fierobe H.-P. , Tardif C. , Sabathe F. , Belaich J.-P. , Belaich A. 
Published: December 2003

ABSTRACT

Clostridium acetobutylicum
ATCC 824 converts sugars and various polysaccharides into acids and solvents. This bacterium, however, is unable to utilize cellulosic substrates, since it is able to secrete very small amounts of cellulosomes. To promote the utilization of crystalline cellulose, the strategy we chose aims at producing heterologous minicellulosomes, containing two different cellulases bound to a miniscaffoldin, in
C. acetobutylicum
. A first step toward this goal describes the production of miniCipC1, a truncated form of CipC from
Clostridium cellulolyticum
, and the hybrid scaffoldin Scaf 3, which bears an additional cohesin domain derived from CipA from
Clostridium thermocellum
. Both proteins were correctly matured and secreted in the medium, and their various domains were found to be functional.
A Mother Cell-Specific Class B Penicillin-Binding Protein, PBP4b, in
Bacillus subtilis
Authors: Wei Yuping , McPherson Derrell C. , Popham David L. 
Published: December 2003

ABSTRACT

The
Bacillus subtilis
genome encodes 16 penicillin-binding proteins (PBPs), some of which are involved in synthesis of the spore peptidoglycan. The
pbpI
(
yrrR
) gene encodes a class B PBP, PBP4b, and is transcribed in the mother cell by RNA polymerase containing σ
E
. Loss of PBP4b, alone and in combination with other sporulation-specific PBPs, had no effect on spore peptidoglycan structure.
An H
+
-Coupled Multidrug Efflux Pump, PmpM, a Member of the MATE Family of Transporters, from
Pseudomonas aeruginosa
Authors: He Gui-Xin , Kuroda Teruo , Mima Takehiko , Morita Yuji , Mizushima Tohru , Tsuchiya Tomofusa 
Published: December 2003

ABSTRACT

We cloned the gene PA1361 (we designated the gene
pmpM
), which seemed to encode a multidrug efflux pump belonging to the MATE family, of
Pseudomonas aeruginosa
by the PCR method using the drug-hypersensitive
Escherichia coli
KAM32 strain as a host. Cells of
E. coli
possessing the
pmpM
gene showed elevated resistance to several antimicrobial agents. We observed energy-dependent efflux of ethidium from cells possessing the
pmpM
gene. We found that PmpM is an H
+
-drug antiporter, and this finding is the first reported case of an H
+
-coupled efflux pump in the MATE family. Disruption and reintroduction of the
pmpM
gene in
P. aeruginosa
revealed that PmpM is functional and that benzalkonium chloride, fluoroquinolones, ethidium bromide, acriflavine, and tetraphenylphosphonium chloride are substrates for PmpM in this microorganism.
Influence of Growth Temperature on Lipid and Phosphate Contents of Surface Polysaccharides from the Antarctic Bacterium
Pseudoalteromonas haloplanktis
TAC 125
Authors: Corsaro M. Michela , Lanzetta Rosa , Parrilli Ermenegilda , Parrilli Michelangelo , Tutino M. Luisa , Ummarino Salvatore 
Published: December 2003

ABSTRACT

The chemical structural variations induced by different growth temperatures in the lipooligosaccharide and exopolysaccharide components extracted from the Antarctic bacterium
Pseudoalteromonas haloplanktis
TAC 125 are described. The increase in phosphorylation with the increase in growth temperature seems to be general, because it happens not only for the lipooligosaccharide but also for the exopolysaccharide. Structural variations in the lipid components of lipid A also occur. In addition, free lipid A is found at both 25 and 4°C but not at 15°C, which is the optimal growth temperature, suggesting a incomplete biosynthesis of the lipooligosaccharide component under the first two temperature conditions.
Characterization of CmaA, an Adenylation-Thiolation Didomain Enzyme Involved in the Biosynthesis of Coronatine
Authors: Couch Robin , O'Connor Sarah E. , Seidle Heather , Walsh Christopher T. , Parry Ronald 
Published: December 2003

ABSTRACT

Several pathovars of
Pseudomonas syringae
produce the phytotoxin coronatine (COR), which contains an unusual amino acid, the 1-amino-2-ethylcyclopropane carboxylic acid called coronamic acid (CMA), which is covalently linked to a polyketide-derived carboxylic acid, coronafacic acid, by an amide bond. The region of the COR biosynthetic gene cluster proposed to be responsible for CMA biosynthesis was resequenced, and errors in previously deposited
cmaA
sequences were corrected. These efforts allowed overproduction of
P. syringae
pv. glycinea PG4180 CmaA in
P. syringae
pv. syringae FF5 as a FLAG-tagged protein and overproduction of
P. syringae
pv. tomato CmaA in
Escherichia coli
as a His-tagged protein; both proteins were in an enzymatically active form. Sequence analysis of CmaA indicated that there were two domains, an adenylation domain (A domain) and a thiolation domain (T domain). ATP-
32
PP
i
exchange assays showed that the A domain of CmaA catalyzes the conversion of branched-chain
l
-amino acids and ATP into the corresponding aminoacyl-AMP derivatives, with a kinetic preference for
l
-
allo-
isoleucine. Additional experiments demonstrated that the T domain of CmaA, which is posttranslationally modified with a 4′-phosphopantetheinyl group, reacts with the AMP derivative of
l
-
allo-
isoleucine to produce an aminoacyl thiolester intermediate. This covalent species was detected by incubating CmaA with ATP and
l
-[G-
3
H]
allo
-isoleucine, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. It is postulated that the
l
-
allo-
isoleucine covalently tethered to CmaA serves as the substrate for additional enzymes in the CMA biosynthetic pathway that catalyze cyclopropane ring formation, which is followed by thiolester hydrolysis, yielding free CMA. The availability of catalytically active CmaA should facilitate elucidation of the details of the subsequent steps in the formation of this novel cyclopropyl amino acid.
Temporal Expression of Pertussis Toxin and Ptl Secretion Proteins byBordetella pertussis
Authors: Rambow-Larsen Amy A. , Weiss Alison A. 
Published: December 2003

ABSTRACTPertussis toxin is an AB5toxin comprised of protein subunits S1 through S5. The individual subunits are secreted by a Sec-dependent mechanism into the periplasm, where the toxin is assembled. The Ptl type IV secretion system mediates secretion of assembled toxin past the outer membrane. In this study, we examined the time course of protein expression, toxin assembly, and secretion as a function of the bacterial growth cycle. Logarithmic growth was observed after a 1-h lag phase. Secreted toxin was first observed at 3 h. Secretion continued throughout the logarithmic growth phase and decreased as the culture entered the stationary phase after about 24 h. On a per cell basis, toxin secretion occurred at a constant rate of 3 molecules/min/cell from 2 to 18 h. More of toxin subunits S1, S2, and S3 were produced than were secreted, resulting in periplasmic accumulation. Periplasmic S1, S2, and S3 were found to be soluble in the periplasm, as well as membrane associated. About one-half of the periplasmic S1, S2 and S3 subunits were incorporated into holotoxin. Secretion component PtlF was present at a low level at time zero, and the level increased between 2 and 24 h from 30 to 1,000 molecules per cell; however, the initial level of PtlF, 30 molecules per cell, supported maximal secretion. The accumulation of both periplasmic toxin and secretion components suggests that translation rates exceed the rate of secretion and that secretion, not toxin and Ptl complex assembly, is rate limiting.
Analysis of Differences in the Functional Properties of the Substrate Binding Proteins of the
Borrelia burgdorferi
Oligopeptide Permease (
opp
) Operon
Authors: Wang Xing-Guo , Kidder J. Michael , Scagliotti Joanna P. , Klempner Mark S. , Noring Richard , Hu Linden T. 
Published: December 2003

ABSTRACT

The
Borrelia burgdorferi
genome encodes five orthologues of the substrate binding protein oligopeptide permease A (OppA). It was previously shown that these genes are under the control of separate promoters and are differentially expressed under various environmental conditions. We were interested in determining whether there are also differences in substrate specificities among the proteins. The substrate specificities of recombinant proteins were determined by screening for high-affinity peptides by use of a combinatorial phage display heptapeptide library. Different heptapeptides with high affinities for OppA-1, OppA-2, and OppA-3 were identified. No heptapeptide binding OppA-4 or OppA-5 could be identified. Competitive binding assays were performed under various conditions to determine the substrate preferences of the OppA proteins. OppA-1 retained maximal activity over a broad range of pHs (5.5 to 7.5), whereas OppA-2 and OppA-3 showed peak activities at pHs below 5.5. OppA-1 and OppA-2 showed preferences for tripeptides over dipeptides and longer-chain peptides. Although a wide variety of amino acyl side chains were tolerated by all three OppA proteins, OppA-1 showed the broadest substrate specificity and was able to accommodate peptides composed of bulky hydrophobic residues; OppA-2 and OppA-3 showed preferences for peptides composed of small nonpolar amino acids. All three OppA proteins showed preferences for peptides composed of
l
- rather than
d
-amino acids. OppA-3 showed the greatest tolerance for changes in stereochemistry. Substantial differences in the substrate specificities of the OppA proteins of
B. burgdorferi
suggest that they may have distinct functions in the organism.
Staphylococcus aureus
Mevalonate Kinase: Isolation and Characterization of an Enzyme of the Isoprenoid Biosynthetic Pathway
Authors: Voynova Natalya E. , Rios Sandra E. , Miziorko Henry M. 
Published: December 2003

ABSTRACT

It has been proposed that isoprenoid biosynthesis in several gram-positive cocci depends on the mevalonate pathway for conversion of acetyl coenzyme A to isopentenyl diphosphate. Mevalonate kinase catalyzes a key reaction in this pathway. In this study the enzyme from
Staphylococcus aureus
was expressed in
Escherichia coli
, isolated in a highly purified form, and characterized. The overall amino acid sequence of this enzyme was very heterologous compared with the sequences of eukaryotic mevalonate kinases. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and analytical gel filtration chromatography suggested that the native enzyme is a monomer with a molecular mass of approximately 33 kDa. The specific activity was 12 U/mg, and the pH optimum was 7.0 to 8.5. The apparent

K
m

values for
R,S
-mevalonate and ATP were 41 and 339 μM, respectively. There was substantial substrate inhibition at millimolar levels of mevalonate. The sensitivity to feedback inhibition by farnesyl diphosphate and its sulfur-containing analog, farnesyl thiodiphosphate, was characterized. These compounds were competitive inhibitors with respect to ATP; the

K
i

values were 46 and 45 μM for farnesyl diphosphate and its thio analog, respectively. Parallel measurements with heterologous eukaryotic mevalonate kinases indicated that
S. aureus
mevalonate kinase is much less sensitive to feedback inhibition (

K
i

difference, 3 orders of magnitude) than the human enzyme. In contrast, both enzymes tightly bound trinitrophenyl-ATP, a fluorescent substrate analog, suggesting that there are similarities in structural features that are important for catalytic function.
RtsA Coordinately Regulates DsbA and theSalmonellaPathogenicity Island 1 Type III Secretion System
Authors: Ellermeier Craig D. , Slauch James M. 
Published: December 2003

ABSTRACTSalmonellaserovars cause a wide variety of diseases ranging from mild gastroenteritis to life-threatening systemic infections. An important step inSalmonella entericaserovar Typhimurium infection is the invasion of nonphagocytic epithelial cells, mediated by a type III secretion system (TTSS) encoded onSalmonellapathogenicity island 1 (SPI1). The SPI1 TTSS forms a needle complex through which effector proteins are injected into the cytosol of host cells, where they promote actin rearrangement and engulfment of the bacteria. We previously identified theSalmonella-specific regulatory protein RtsA, which induces expression ofhilAand, thus, the SPI1 genes. Here we show that thehilAregulators RtsA, HilD, and HilC can each induce transcription ofdsbA, which encodes a periplasmic disulfide bond isomerase. RtsA induces expression ofdsbAindependent of either the SPI1 TTSS or the only known regulator ofdsbA, the CpxRA two-component system. We show that DsbA is required for both the SPI1 and SPI2 TTSS to translocate effector proteins into the cytosol of host cells. DsbA is also required for survival during the systemic stages of infection. We also present evidence that production of SPI1 effector proteins is coupled to assembly of the TTSS. This feedback regulation is mediated at either the transcriptional or posttranscriptional level, depending on the particular effector. Loss of DsbA leads to feedback inhibition, which is consistent with the hypothesis that disulfide bond formation plays a role in TTSS assembly or function.
Production of Muramic δ-Lactam in
Bacillus subtilis
Spore Peptidoglycan
Authors: Gilmore Meghan E. , Bandyopadhyay Dabanjan , Dean Amanda M. , Linnstaedt Sarah D. , Popham David L. 
Published: December 2003

ABSTRACT

Bacterial spore heat resistance is primarily dependent upon dehydration of the spore cytoplasm, a state that is maintained by the spore peptidoglycan wall, the spore cortex. A peptidoglycan structural modification found uniquely in spores is the formation of muramic δ-lactam. Production of muramic δ-lactam in
Bacillus subtilis
requires removal of a peptide side chain from the
N
-acetylmuramic acid residue by a
cwlD
-encoded muramoyl-
l
-Alanine amidase. Expression of
cwlD
takes place in both the mother cell and forespore compartments of sporulating cells, though expression is expected to be required only in the mother cell, from which cortex synthesis derives. Expression of
cwlD
in the forespore is in a bicistronic message with the upstream gene
ybaK
. We show that
ybaK
plays no apparent role in spore peptidoglycan synthesis and that expression of
cwlD
in the forespore plays no significant role in spore peptidoglycan formation. Peptide cleavage by CwlD is apparently followed by deacetylation of muramic acid and lactam ring formation. The product of
pdaA
(
yfjS
), which encodes a putative deacetylase, has recently been shown to also be required for muramic δ-lactam formation. Expression of CwlD in
Escherichia coli
results in muramoyl
l
-Alanine amidase activity but no muramic δ-lactam formation. Expression of PdaA alone in
E. coli
had no effect on
E. coli
peptidoglycan structure, whereas expression of CwlD and PdaA together resulted in the formation of muramic δ-lactam. CwlD and PdaA are necessary and sufficient for muramic δ-lactam production, and no other
B. subtilis
gene product is required. PdaA probably carries out both deacetylation and lactam ring formation and requires the product of CwlD activity as a substrate.
NpdR, a Repressor Involved in 2,4,6-Trinitrophenol Degradation in
Rhodococcus opacus
HL PM-1
Authors: Nga Dang P. , Altenbuchner Josef , Heiss Gesche S. 
Published: December 2003

ABSTRACT

Rhodococcus opacus
HL PM-1 utilizes 2,4,6-trinitrophenol (picric acid) as a sole nitrogen source. The initial attack on picric acid occurs through two hydrogenation reactions. Hydride transferase II (encoded by
npdI
) and hydride transferase I (encoded by
npdC
) are responsible for the hydride transfers. Database searches with the
npd
genes have indicated the presence of a putative transcriptional regulator,
npdR
. Here, the
npdR
gene was expressed in
Escherichia coli
, and the protein was purified and shown to form a complex with intergenic regions between open reading frames A and B and between
npdH
and
npdI
within the
npd
gene cluster. A change in DNA-NpdR complex formation occurred in the presence of 2,4-dinitrophenol, picric acid, 2-chloro-4,6-dinitrophenol, and 2-methyl-4,6-dinitrophenol. By constructing a promoter-probe vector, we demonstrated that both intergenic regions caused the expression of reporter gene
xylE
. Hence, both of these regions contain promoters. A deletion mutant of
R. opacus
HL PM-1 was constructed in which part of
npdR
was deleted. The expression of
npdI
and
npdC
was induced by 2,4-dinitrophenol in the wild-type strain, while in the mutant these genes were constitutively expressed. Hence, NpdR is a repressor involved in picric acid degradation.
MICHEL TRĀD, IN MEMORIAM
Authors: Kallas Elie 
Published: December 2003

AbstractMichel Trād (1912-1998), pionnier de la littérature vernaculaire libanaise du 20ème siècle, a conclu sa vie simple et pleine d'émerveillement, déçu par la modernité et par l'homme. Certains de ses poèmes - chantés par Fayrūz et Wad' al-Sāfī - ont fait le tour du monde néo-arabophone, mais à ce jour, aucun de ses recueils n'a été traduit. Cet article le commémore et tente de nous faire savourer son art, plaide pour son réalisme linguistique et sa spontanéité lyrique, illustre la potentialité métaphorique de ses mots-clefs, sans négliger la prosodie des vers. L'annexe comprend quelques traductions de poèmes extraits de son recueil Guélnār.
VOM SINN DER ZEIT AUS DER GESCHICHTE DES ARABISCHEN CHRONOGRAMMS
Authors: Bauer Thomas 
Published: December 2003

AbstractLe sens du temps. Pages d'histoire du chronogramme arabe». Après des antécédents encore mal connus au VIIe/XIIIe siècle et au VIIIe/XIVe siècle, les chronogrammes «réguliers» sont bien attestés en arabe au IXe/XVe siècle; mais leur véritable carrière commença au Xe/XVIe siècle. Par la suite, les poètes, compositeurs de ce genre, s'imposèrent sont ici étudiés non seulement la structure et les occasions de ces poèmes, mais aussi leur évolution et la fascination que ce type d'écriture exerça.