bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Phenotypic Analysis of theBordetella parapertussisIsolate Chosen for Genomic Sequencing
Authors: Heininger Ulrich , Cotter Peggy A. , Fescemyer Howard W. , Martinez de Tejada Guillermo , Yuk Ming H. , Miller Jeff F. , Harvill Eric T. 
Published: July 2002

ABSTRACTThe genomes of three closely related bordetellae are currently being sequenced, thus providing an opportunity for comparative genomic approaches driven by an understanding of the comparative biology of these three bacteria. Although the other strains being sequenced are well studied, the strain ofBordetella parapertussischosen for sequencing is a recent human clinical isolate (strain 12822) that has yet to be characterized in detail. This investigation reports the first phenotypic characterization of this strain, which will likely become the prototype for this species in comparison with the prototype strains ofB. pertussis(Tohama I),B. bronchiseptica(RB50), and other isolates ofB. parapertussis. Multiple in vitro and in vivo assays distinguished each species.B. parapertussiswas more similar toB. bronchisepticathan toB. pertussisin many assays, including in BvgS signaling characteristics, presence of urease activity, regulation of urease expression by BvgAS, virulence in the respiratory tracts of immunocompromised mice, induction of anti-Bordetellaantibodies, and serum antimicrobial resistance. In other assays,B. parapertussiswas distinct from all other species (in pigment production) or more similar toB. pertussis(by lack of motility and cytotoxicity to a macrophage-like cell line). These results begin to provide phenotypes that can be related to genetic differences identified in the genomic sequences of bordetellae.
In Vivo Effects of a Synthetic 2-Kilodalton Macrophage-Activating Lipopeptide ofMycoplasma fermentansafter Pulmonary Application
Authors: Lührmann Anke , Deiters Ursula , Skokowa Julia , Hanke Michaela , Gessner Johannes E. , Mühlradt Peter F. , Pabst Reinhard , Tschernig Thomas 
Published: July 2002

ABSTRACTMycoplasmas can cause interstitial pneumonias inducing critical illness in humans and animals. Mycoplasma infections are characterized by an influx of neutrophils, followed by an accumulation of macrophages and lymphocytes. The present study deals with the question of which mycoplasmal components cause this host reaction. The mycoplasma-derived, macrophage-activating lipopeptide 2S-MALP-2 was used to mimic the sequelae of a mycoplasma infection. To this end, 2S-MALP-2 was intratracheally instilled into the lungs of Lewis rats, and the bronchoalveolar lavage cells were examined at different times after different doses of 2S-MALP-2. Application of 2.5 μg induced a pronounced leukocyte accumulation in the bronchoalveolar space. At 24 h after 2S-MALP-2 administration, the majority of leukocytes consisted of neutrophils, followed by macrophages, peaking on days 2 and 3. Lymphocyte numbers, although amounting to only a few percent of the total bronchoalveolar lavage cells, also increased significantly, with maximal lymphocyte accumulation occurring by 72 h after instillation. The leukocyte count of the lung interstitium was increased on day 3 after treatment. After 10 days all investigated cell populations returned to control levels. Transient chemotactic activity for neutrophils was detected in the bronchoalveolar lavage fluid early after 2S-MALP-2 application, followed by monocyte chemoattractant protein-1 activity (MCP-1) in lung homogenates. MCP-1 was produced by bronchoalveolar lavage cells upon stimulation with 2S-MALP-2. Our data indicate that mycoplasmal lipoproteins and lipopeptides are probably the most relevant mycoplasmal components for the early host reaction. The primary target cells are likely to be the alveolar macrophages liberating chemokines, which attract further leukocytes.
Progressive Bovine Paratuberculosis Is Associated with Local Loss of CD4+T Cells, Increased Frequency of γδ T Cells, and Related Changes in T-Cell Function
Authors: Koets Ad , Rutten Victor , Hoek Aad , van Mil Frans , Müller Kerstin , Bakker Douwe , Gruys Erik , van Eden Willem 
Published: July 2002

ABSTRACTBovine paratuberculosis is caused by the infection of young calves withMycobacterium aviumsubsp.paratuberculosis, resulting in a chronic granulomatous infection of predominantly the ileum. After an incubation period of 2 to 5 years, the disease becomes progressive in some of the chronically infected, but asymptomatic cows. This results in a protein-losing enteropathy that will ultimately be fatal. A loss of cell-mediated immune responses in symptomatic animals has been described, but no information is available concerning immune reactivity in the intestine. We sought to investigate putative disease status-associated lymphocyte subset distributions and antigen-specific functional characteristics of mononuclear cells isolated from blood, gut-associated lymphoid tissue, and the intestinal walls of 22 cows in different stages of disease and in control animals. The results demonstrated a significant decrease in CD4+T-cell frequency and a significant increase in TcR1-N12+γδ T-cell frequency in ileum lamina propria lymphocytes of symptomatic animals compared to the asymptomatic shedders. Immunohistology revealed that there was also an absolute decrease in the number of CD4+T cells in sections of the lesional ileum. Our findings also indicated that both peripheral and intestinal cell-mediated responses are decreased in symptomatic animals compared to asymptomatic animals. We conclude that the decrease in cell-mediated responses is likely related to a loss of antigen-specific CD4+T cells, which is most prominent in the lesional ileum from symptomatic animals, thus contributing to the progressive nature of bovine paratuberculosis.
Characterization of the Fructosyltransferase Gene of
Actinomyces naeslundii
WVU45
Authors: Bergeron Lori J. , Morou-Bermudez Evangelia , Burne Robert A. 
Published: July 2002

ABSTRACT

Oral actinomycetes produce fructosyltransferase (FTF) enzymes which convert sucrose into polymers of
d
-fructose, known as levans, and these polymers are thought to contribute to the persistence and virulence of the organisms. A gene encoding FTF was isolated from
Actinomyces naeslundii
WVU45; the deduced amino acid sequence showed significant similarity to known levansucrases of gram-negative environmental isolates but was less similar to FTFs from gram-positive bacteria. A transcriptional start site was mapped by primer extension 70 bp 5′ from the putative start codon. Promoter fusions to a chloramphenicol acetyltransferase gene were used to confirm that there was a functional promoter driving
ftf
expression and to show that sequences located 86 to 218 bp upstream of the transcription initiation site were required for optimal
ftf
expression. Quantitative slot blot analysis against total RNA from cells grown on different sugars or from different growth phases revealed that
ftf
was constitutively transcribed. Thus, the
A. naeslundii
FTF is more similar in primary sequence and the regulation of expression to levansucrases of gram-negative bacteria than gram-positive bacteria.
Decoupling of Genome Size and Sequence Divergence in a Symbiotic Bacterium
Authors: Wernegreen Jennifer J. , Ochman Howard , Jones Isaac B. , Moran Nancy A. 
Published: July 2002

ABSTRACT

In contrast to genome size variation in most bacterial taxa, the small genome size of
Buchnera
sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). This exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign DNA and reduced selection for genetic novelty within a static intracellular environment.
SecB Dependence of an Exported Protein Is a Continuum Influenced by the Characteristics of the Signal Peptide or Early Mature Region
Authors: Kim Jinoh , Luirink Joen , Kendall Debra A. 
Published: July 2002

ABSTRACT

We have used
Escherichia coli
alkaline phosphatase to show the interplay among the characteristics of two amino-terminal domains in the preprotein (the signal peptide and the early mature region), the efficiency with which this protein is transported, and its requirement for SecB to accomplish the transport process. The results suggest that although alkaline phosphatase does not normally require SecB for transport, it is inherently able to utilize SecB, and it does so when its ability to interface with the transport machinery is compromised.
Identification of a Second Region of the Spo0A Response Regulator of
Bacillus subtilis
Required for Transcription Activation
Authors: Rowe-Magnus Dean A. , Richer Martin J. , Spiegelman George B. 
Published: July 2002

ABSTRACT

Deletion of the 10 C-terminal amino acids of the
Bacillus subtilis
response regulator Spo0A or valine substitution at D258 and L260 resulted in a sporulation-negative phenotype and loss of in vivo activation of the
spoIIG
and
spoIIA
operon promoters. Repression of the
abrB
promoter was not affected by the mutations. In combination with the previously characterized mutation (A257V), the results identify amino acids at positions 257, 258, and 260 as being required for transcription activation by Spo0A.
Autoregulation of the
Pseudomonas aeruginosa
Protein PtxS Occurs through a Specific Operator Site within the
ptxS
Upstream Region
Authors: Swanson Britta L. , Hamood Abdul N. 
Published: July 2002

ABSTRACT

We have previously shown that the
Pseudomonas aeruginosa toxA
regulatory protein PtxS autoregulates its own synthesis by binding to a 52-bp fragment. The 3′ end of the 52-bp fragment is located 58 bp 5′ of the
ptxS
translation start site. We have identified a 14-bp palindromic sequence (TGAAACCGGTTTCA) within the 52-bp fragment. In this study, we used site-directed mutagenesis and promoter fusion experiments to determine if PtxS binds specifically to this palindromic sequence and regulates
ptxS
expression. We have also tried to determine the roles of specific nucleotides within the palindromic sequence in PtxS binding and
ptxS
expression. Initial promoter fusion experiments confirmed that the 52-bp fragment does not overlap with the region that carries the
ptxS
promoter activity. PtxS binding was eliminated upon the deletion of the 14-bp palindromic sequence from the 52-bp fragment. In addition, the deletion of the 14-bp sequence caused a significant enhancement in
ptxS
expression in the
P. aeruginosa
strain PAO1 and the
ptxS
isogenic mutant PAO::
ptxS
. Mutation of specific nucleotides within the 14-bp sequence eliminated, reduced, or had no effect on PtxS binding. However, mutations of several of these nucleotides produced a significant increase in
ptxS
expression in both PAO1 and PAO::
ptxS
. These results suggest that (i) the 14-bp palindromic sequence and specific nucleotides within it play a role in PtxS binding and (ii) deletion of the palindromic sequence or changing of certain nucleotides within it interferes with another mechanism that may regulate
ptxS
expression.
Gene Expression Analysis of the
Streptococcus pneumoniae
Competence Regulons by Use of DNA Microarrays
Authors: Peterson Scott , Cline Robin T. , Tettelin Hervé , Sharov Vasily , Morrison Donald A. 
Published: July 2002

ABSTRACT

Competence for genetic transformation in
Streptococcus pneumoniae
is coordinated by the competence-stimulating peptide (CSP), which induces a sudden and transient appearance of competence during exponential growth in vitro. Models of this quorum-sensing mechanism have proposed sequential expression of several regulatory genes followed by induction of target genes encoding DNA-processing-pathway proteins. Although many genes required for transformation are known to be expressed only in response to CSP, the relative timing of their expression has not been established. Overlapping expression patterns for the genes
cinA
and
comD
(G. Alloing, B. Martin, C. Granadel, and J. P. Claverys, Mol. Microbiol. 29:75–83, 1998) suggest that at least two distinct regulatory mechanisms may underlie the competence cycle. DNA microarrays were used to estimate mRNA levels for all known competence operons during induction of competence by CSP. The known competence regulatory operons,
comAB
,
comCDE
, and
comX
, exhibited a low or zero initial (uninduced) signal, strongly increased expression during the period between 5 and 12 min after CSP addition, and a decrease nearly to original values by 15 min after initiation of exposure to CSP. The remaining competence genes displayed a similar expression pattern, but with an additional delay of approximately 5 min. In a mutant defective in ComX, which may act as an alternate sigma factor to allow expression of the target competence genes, the same regulatory genes were induced, but the other competence genes were not. Finally, examination of the expression of 60 candidate sites not previously associated with competence identified eight additional loci that could be induced by CSP.
The Level of
DAL80
Expression Down-Regulates GATA Factor-Mediated Transcription in
Saccharomyces cerevisiae
Authors: Cunningham Thomas S. , Rai Rajendra , Cooper Terrance G. 
Published: July 2002

ABSTRACT

Nitrogen-catabolic gene expression in
Saccharomyces cerevisiae
is regulated by the action of four GATA family transcription factors: Gln3p and Gat1p/Nil1p are transcriptional activators, and Dal80 and Deh1p/Gzf3p are repressors. In addition to the GATA sequences situated upstream of all nitrogen catabolite repression-sensitive genes that encode enzyme and transport proteins, the promoters of the
GAT1
,
DAL80
, and
DEH1
genes all contain multiple GATA sequences as well. These GATA sequences are the binding sites of the GATA family transcription factors and are hypothesized to mediate their autogenous and cross regulation. Here we show, using
DAL80
fused to the carbon-regulated
GAL1
,
10
or copper-regulated
CUP1
promoter, that
GAT1
expression is inversely regulated by the level of
DAL80
expression, i.e., as
DAL80
expression increases,
GAT1
expression decreases. The amount of
DAL80
expression also dictates the level at which
DAL3
, a gene activated almost exclusively by Gln3p, is transcribed. Gat1p was found to partially substitute for Gln3p in transcription. These data support the contention that regulation of GATA-factor gene expression is tightly and dynamically coupled. Finally, we suggest that the complicated regulatory circuit in which the GATA family transcription factors participate is probably most beneficial as cells make the transition from excess to limited nitrogen availability.
A Gene Cluster Involved in Metal Homeostasis in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803
Authors: García-Domínguez Mario , Lopez-Maury Luis , Florencio Francisco J. , Reyes José C. 
Published: July 2002

ABSTRACT

A gene cluster composed of nine open reading frames (ORFs) involved in Ni
2+
, Co
2+
, and Zn
2+
sensing and tolerance in the cyanobacterium
Synechocystis
sp. strain PCC 6803 has been identified. The cluster includes an Ni
2+
response operon and a Co
2+
response system, as well as a Zn
2+
response system previously described. Expression of the Ni
2+
response operon (
nrs
) was induced in the presence of Ni
2+
and Co
2+
. Reduced Ni
2+
tolerance was observed following disruption of two ORFs of the operon (
nrsA
and
nrsD
). We also show that the
nrsD
gene encodes a putative Ni
2+
permease whose carboxy-terminal region is a metal binding domain. The Co
2+
response system is composed of two divergently transcribed genes,
corR
and
corT
, mutants of which showed decreased Co
2+
tolerance. Additionally,
corR
mutants showed an absence of Co
2+
-dependent induction of
corT
, indicating that CorR is a transcriptional activator of
corT
. To our knowledge, CorR is the first Co
2+
-sensing transcription factor described. Our data suggest that this region of the
Synechocystis
sp. strain PCC 6803 genome is involved in sensing and homeostasis of Ni
2+
, Co
2+
, and Zn
2+
.
Dual Roles of
Bradyrhizobium japonicum
Nickelin Protein in Nickel Storage and GTP-Dependent Ni Mobilization
Authors: Olson Jonathan W. , Maier Robert J. 
Published: July 2002

ABSTRACT

The hydrogenase accessory protein HypB, or nickelin, has two functions in the N
2
-fixing, H
2
-oxidizing bacterium
Bradyrhizobium japonicum
. One function of HypB involves the mobilization of nickel into hydrogenase. HypB also carries out a nickel storage/sequestering function in
B. japonicum
, binding nine nickel ions per monomer. Here we report that the two roles (nickel mobilization and storage) of HypB can be separated in vitro and in vivo using molecular and biochemical approaches. The role of HypB in hydrogenase maturation is completely dependent on its intrinsic GTPase activity; strains which produce a HypB protein that is severely deficient in GTPase activity but that fully retains nickel-sequestering ability cannot produce active hydrogenase even upon prolonged nickel supplementation. A HypB protein that lacks the nickel-binding polyhistidine region near the N terminus lacks only the nickel storage capacity function; it is still able to bind a single nickel ion and also retains complete GTPase activity.
A C-Terminal Disulfide Bridge in Pediocin-Like Bacteriocins Renders Bacteriocin Activity Less Temperature Dependent and Is a Major Determinant of the Antimicrobial Spectrum
Authors: Fimland Gunnar , Johnsen Line , Axelsson Lars , Brurberg May B. , Nes Ingolf F. , Eijsink Vincent G. H. , Nissen-Meyer Jon 
Published: July 2002

ABSTRACT
Several lactic acid bacteria produce so-called pediocin-like bacteriocins that share sequence characteristics, but differ in activity and target cell specificity. The significance of a C-terminal disulfide bridge present in only a few of these bacteriocins was studied by site-directed mutagenesis of pediocin PA-1 (which naturally contains the bridge) and sakacin P (which lacks the bridge). Introduction of the C-terminal bridge into sakacin P broadened the target cell specificity of this bacteriocin, as illustrated by the fact that the mutants were 10 to 20 times more potent than the wild-type toward certain indicator strains, whereas the potency toward other indicator strains remained essentially unchanged. Like pediocin PA-1, disulfide-containing sakacin P mutants had the same potency at 20 and 37°C, whereas wild-type sakacin P was approximately 10 times less potent at 37°C than at 20°C. Reciprocal effects on target cell specificity and the temperature dependence of potency were observed upon studying the effect of removing the C-terminal disulfide bridge from pediocin PA-1 by Cys→Ser mutations. These results clearly show that a C-terminal disulfide bridge in pediocin-like bacteriocins contributes to widening of the antimicrobial spectrum as well as to higher potency at elevated temperatures. Interestingly, the differences between sakacin P and pediocin PA-1 in terms of the temperature dependency of their activities correlated well with the optimal temperatures for bacteriocin production and growth of the bacteriocin-producing strain.
Expression of UGA-Containing
Mycoplasma
Genes in
Bacillus subtilis
Authors: Kannan T. R. , Baseman Joel B. 
Published: July 2002

ABSTRACT

We used
Bacillus subtilis
to express UGA-containing
Mycoplasma
genes encoding the P30 adhesin (one UGA) of
Mycoplasma pneumoniae
and methionine sulfoxide reductase (two UGAs) of
Mycoplasma genitalium
. Due to natural UGA suppression, these
Mycoplasma
genes were expressed as full-length protein products, but at relatively low efficiency, in recombinant wild-type
Bacillus
. The
B. subtilis
-expressed
Mycoplasma
proteins appeared as single bands and not as multiple bands compared to expression in recombinant
Escherichia coli. Bacillus
mutants carrying mutations in the structural gene (
prfB
) for release factor 2 markedly enhanced the level of readthrough of UGA-containing
Mycoplasma
genes.
Rubrerythrin and Rubredoxin Oxidoreductase inDesulfovibrio vulgaris: a Novel Oxidative Stress Protection System
Authors: Lumppio Heather L. , Shenvi Neeta V. , Summers Anne O. , Voordouw Gerrit , Kurtz Donald M. 
Published: July 2002

ABSTRACTEvidence is presented for an alternative to the superoxide dismutase (SOD)-catalase oxidative stress defense system inDesulfovibrio vulgaris(strain Hildenborough). This alternative system consists of the nonheme iron proteins, rubrerythrin (Rbr) and rubredoxin oxidoreductase (Rbo), the product of therbogene (also called desulfoferrodoxin). A Δrbostrain ofD. vulgariswas found to be more sensitive to internal superoxide exposure than was the wild type. Unlike Rbo, expression of plasmid-borne Rbr failed to restore the aerobic growth of a SOD-deficient strain ofEscherichia coli. Conversely, plasmid-borne expression of two different Rbrs fromD. vulgarisincreased the viability of a catalase-deficient strain ofE. colithat had been exposed to hydrogen peroxide whereas Rbo actually decreased the viability. A previously undescribedD. vulgarisgene was found to encode a protein having 50% sequence identity to that ofE. coliFe-SOD. This gene also encoded an extended N-terminal sequence with high homologies to export signal peptides of periplasmic redox proteins. The SOD activity ofD. vulgarisis not affected by the absence of Rbo and is concentrated in the periplasmic fraction of cell extracts. These results are consistent with a superoxide reductase rather than SOD activity of Rbo and with a peroxidase activity of Rbr. A joint role for Rbo and Rbr as a novel cytoplasmic oxidative stress protection system inD. vulgarisand other anaerobic microorganisms is proposed.
β-Ketoacyl Acyl Carrier Protein Synthase III (FabH) Is Essential for Fatty Acid Biosynthesis in
Streptomyces coelicolor
A3(2)
Authors: Revill W. Peter , Bibb Maureen J. , Scheu Ann-Karolin , Kieser Helen J. , Hopwood David A. 
Published: July 2002

ABSTRACT

The
Streptomyces coelicolor fab
(fatty acid biosynthesis) gene cluster (
fabD-fabH-acpP-fabF
) is cotranscribed to produce a leaderless mRNA transcript. One of these genes,
fabH
, encodes a ketoacyl synthase III that is essential to and is proposed to be responsible for initiation of fatty acid biosynthesis in
S. coelicolor
.
Virulence Plasmid-Borne
spvB
and
spvC
Genes Can Replace the 90-Kilobase Plasmid in Conferring Virulence to
Salmonella enterica
Serovar Typhimurium in Subcutaneously Inoculated Mice
Authors: Matsui Hidenori , Bacot Christopher M. , Garlington Wendy A. , Doyle Thomas J. , Roberts Steve , Gulig Paul A. 
Published: July 2002

ABSTRACT

In a mouse model of systemic infection, the
spv
genes carried on the
Salmonella enterica
serovar Typhimurium virulence plasmid increase the replication rate of salmonellae in host cells of the reticuloendothelial system, most likely within macrophages. A nonpolar deletion in the
spvB
gene greatly decreased virulence but could not be complemented by
spvB
alone. However, a low-copy-number plasmid expressing
spvBC
from a constitutive
lacUV5
promoter did complement the
spvB
deletion. By examining a series of
spv
mutations and cloned
spv
sequences, we deduced that
spvB
and
spvC
could be sufficient to confer plasmid-mediated virulence to
S. enterica
serovar Typhimurium. The
spvBC
-bearing plasmid was capable of replacing all of the
spv
genes, as well as the entire virulence plasmid, of serovar Typhimurium for causing systemic infection in BALB/c mice after subcutaneous, but not oral, inoculation. A point mutation in the
spvBC
plasmid preventing translation but not transcription of
spvC
eliminated the ability of the plasmid to confer virulence. Therefore, it appears that both
spvB
and
spvC
encode the principal effector factors for Spv- and plasmid-mediated virulence of serovar Typhimurium.