bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmentally regulated expression of mouse HtrA3 and its role as an inhibitor of TGF‐β signaling
Authors: Tocharus Jiraporn , Tsuchiya Akiho , Kajikawa Miwa , Ueta Yoshifumi , Oka Chio , Kawaichi Masashi 
Published: June 2004

The expression of mouse HtrA1 is developmentally regulated and restricted in embryo tissues which depend largely on TGF‐β signaling for their differentiation. We examined whether mouse HtrA3, another HtrA family member very close to HtrA1, shows similar expression patterns. HtrA3 and ‐1 were expressed mostly in the same embryonic organs but exhibited complementary patterns in various tissues; the lens epithelial cells in day 12.5 embryo expressed HtrA3 whereas the ciliary body and pigment retina expressed HtrA1. In the vertebrae of day 14.5 embryo, HtrA3 was expressed in the tail region, but HtrA1 was predominantly expressed in the thoracic and lumbar regions.Similar to HtrA1, HtrA3 bound to various TGF‐β proteins and inhibited the signaling of BMP‐4, ‐2 and TGF‐β1. HtrA3 did not inhibit signaling originated from a constitutively active BMP receptor, indicating that the inhibition occurred upstream of the cell surface receptor. HtrA3 also showed proteolytic activities indistinguishable from those of HtrA1 toward β‐casein and some extracellular matrix (ECM) proteoglycans. The protease activity was absolutely required for the TGF‐β signal inhibition activity.All these data suggest that HtrA3 and ‐1 have the overlapping biological activities but can function in complementary fashion in certain types of tissues.
Microarray-Based Analysis of theStaphylococcus aureusσBRegulon
Authors: Bischoff Markus , Dunman Paul , Kormanec Jan , Macapagal Daphne , Murphy Ellen , Mounts William , Berger-Bächi Brigitte , Projan Steven 
Published: June 2004

ABSTRACTMicroarray-based analysis of the transcriptional profiles of the genetically distinctStaphylococcus aureusstrains COL, GP268, and Newman indicate that a total of 251 open reading frames (ORFs) are influenced by σBactivity. While σBwas found to positively control 198 genes by a factor of ≥2 in at least two of the three genetic lineages analyzed, 53 ORFs were repressed in the presence of σB. Gene products that were found to be influenced by σBare putatively involved in all manner of cellular processes, including cell envelope biosynthesis and turnover, intermediary metabolism, and signaling pathways. Most of the genes and/or operons identified as upregulated by σBwere preceded by a nucleotide sequence that resembled the σBconsensus promoter sequence ofBacillus subtilis. A conspicuous number of virulence-associated genes were identified as regulated by σBactivity, with many adhesins upregulated and prominently represented in this group, while transcription of various exoproteins and toxins were repressed. The data presented here suggest that the σBofS. aureuscontrols a large regulon and is an important modulator of virulence gene expression that is likely to act conversely to RNAIII, the effector molecule of theagrlocus. We propose that this alternative transcription factor may be of importance for the invading pathogen to fine-tune its virulence factor production in response to changing host environments.
Telomere Exchange between Linear Replicons ofBorrelia burgdorferi
Authors: Huang Wai Mun , Robertson Margaret , Aron John , Casjens Sherwood 
Published: June 2004

ABSTRACTSpirochetes in the genusBorreliacarry a linear chromosome and numerous linear plasmids that have covalently closed hairpin telomeres. The overall organization of the large chromosome ofBorrelia burgdorferiappears to have been quite stable over recent evolutionary time; however, a large fraction of natural isolates carry differing lengths of DNA that extend the right end of the chromosome between about 7 and 20 kbp relative to the shortest chromosomes. We present evidence here that a rather recent nonhomologous recombination event in theB. burgdorferistrain Sh-2-82 lineage has replaced its right chromosomal telomere with a large portion of the linear plasmid lp21, which is present in the strain B31 lineage. At least two successive rounds of addition of linear plasmid genetic material to the chromosomal right end appear to have occurred at the Sh-2-82 right telomere, suggesting that this is an evolutionary mechanism by which plasmid genetic material can become part of the chromosome. The unusual nonhomologous nature of this rearrangement suggests that, barring horizontal transfer, it can be used as a unique genetic marker for this lineage ofB. burgdorferichromosomes.
Presence of a Novel Phosphopentomutase and a 2-Deoxyribose 5-Phosphate Aldolase Reveals a Metabolic Link between Pentoses and Central Carbon Metabolism in the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
Authors: Rashid Naeem , Imanaka Hiroyuki , Fukui Toshiaki , Atomi Haruyuki , Imanaka Tadayuki 
Published: June 2004

ABSTRACT

Numerous bacteria and mammalian cells harbor two enzymes, phosphopentomutase (PPM) and 2-deoxyribose 5-phosphate aldolase (DERA), involved in the interconversion between nucleosides and central carbon metabolism. In this study, we have examined the presence of this metabolic link in the hyperthermophilic archaeon,
Thermococcus kodakaraensis
KOD1. A search of the genome sequence of this strain revealed the presence of a closely related orthologue (TK2104) of bacterial DERA genes while no orthologue related to previously characterized PPM genes could be detected. Expression, purification, and characterization of the TK2104 protein product revealed that this gene actually encoded a DERA, catalyzing the reaction through a class I aldolase mechanism. As PPM activity was detected in
T. kodakaraensis
cells, we partially purified the protein to examine its N-terminal amino acid sequence. The sequence corresponded to a gene (TK1777) similar to phosphomannomutases within COG1109 but not COG1015, which includes all previously identified PPMs. Heterologous gene expression of TK1777 and characterization of the purified recombinant protein clearly revealed that the gene indeed encoded a PPM. Both enzyme activities could be observed in
T. kodakaraensis
cells under glycolytic and gluconeogenic growth conditions, whereas the addition of ribose, 2-deoxyribose, and 2′-deoxynucleosides in the medium did not lead to a significant induction of these activities. Our results clearly indicate the presence of a metabolic link between pentoses and central carbon metabolism in
T. kodakaraensis
, providing an alternative route for pentose biosynthesis through the functions of DERA and a structurally novel PPM.
Identification of Inducers of the
Yersinia enterocolitica
Phage Shock Protein System and Comparison to the Regulation of the RpoE and Cpx Extracytoplasmic Stress Responses
Authors: Maxson Michelle E. , Darwin Andrew J. 
Published: June 2004

ABSTRACT

Known inducers of the phage shock protein (Psp) system suggest that it is an extracytoplasmic stress response, as are the well-studied RpoE and Cpx systems. However, a random approach to identify conditions and proteins that induce the Psp system has not been attempted. It is also unknown whether the proteins or mutations that induce Psp are specific or if they also activate the RpoE and Cpx systems. This study addressed these issues for the
Yersinia enterocolitica
Psp system. Random transposon mutagenesis identified null mutations and overexpression mutations that increase Φ(
pspA
-
lacZ
) operon fusion expression. The results suggest that Psp may respond exclusively to extracytoplasmic stress. Null mutations affected glucosamine-6-phosphate synthetase (
glmS
), which plays a role in cell envelope biosynthesis, and the F
0
F
1
ATPase (
atp
operon). The screen also revealed that in addition to several secretins, the overexpression of three novel putative inner membrane proteins (IMPs) induced the Psp response. We also compared induction of the
Y. enterocolitica
Psp, RpoE, and Cpx responses. Overexpression of secretins or the three IMPs or the presence of an
atpB
null mutation only induced the Psp response. Similarly, known inducers of the RpoE and Cpx responses did not significantly induce the Psp response. Only the
glmS
null mutation induced all three responses. Therefore, Psp is induced distinctly from the RpoE and Cpx systems. The specific IMP inducers may be valuable tools to probe specific signal transduction events of the Psp response in future studies.
Regulation of Expression of Cellulosomes and Noncellulosomal (Hemi)Cellulolytic Enzymes in
Clostridium cellulovorans
during Growth on Different Carbon Sources
Authors: Han Sung Ok , Cho Hee-Yeon , Yukawa Hideaki , Inui Masayuki , Doi Roy H. 
Published: June 2004

ABSTRACT

Cellulosomes and noncellulosomal (hemi)cellulolytic enzymes are produced by
Clostridium cellulovorans
to degrade plant cell walls. To understand their synergistic relationship, changes in mRNA and protein expression in cellulosomes and noncellulosomal (hemi)cellulolytic enzymes (hereafter called noncellulosomal enzymes) of cultures grown on cellobiose, cellulose, pectin, xylan, and corn fiber or mixtures thereof were examined. Cellulase expression, favored particularly by the presence of Avicel, was found with all substrates. Comparison of cellulosome and noncellulosomal enzymes showed that expression profiles were strongly affected by the carbon source. High xylanase or pectate lyase expression was observed when
C. cellulovorans
was grown on xylan or pectin, respectively. Mixed carbon substrates (cellulose-pectin-xylan mixture or corn fiber) induced a wider variety of enzymes than a single carbon source, such as cellobiose, pectin, or xylan. Cellulosomal proteome profiles were more affected by the carbon source than the noncellulosomal enzymes. Transcription and protein analyses revealed that cellulosomes and noncellulosomal enzymes were expressed simultaneously on mixed carbon sources, but their degree of inducibility varied when the substrate was either cellulose or cellobiose. Cellulosomes and noncellulosomal enzymes had synergistic activity on various carbon substrates. These results indicated that expression of plant cell wall-degrading enzymes is highly influenced by the available carbon source and that synergy between cellulosomes and noncellulosomal enzymes contribute to plant cell wall degradation.
Structure of
Pseudomonas aeruginosa
Populations Analyzed by Single Nucleotide Polymorphism and Pulsed-Field Gel Electrophoresis Genotyping
Authors: Morales Gracia , Wiehlmann Lutz , Gudowius Peter , van Delden Christian , Tümmler Burkhard , Martínez José Luis , Rojo Fernando 
Published: June 2004

ABSTRACT

Pseudomonas aeruginosa
has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of
P. aeruginosa
, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (
oriC
,
oprL
,
fliC
,
alkB2
,
citS
,
oprI
, and
ampC
). The combination of these SNPs plus the type of
fliC
present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of
P. aeruginosa
strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The
P. aeruginosa
chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the
P. aeruginosa
population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.
Multiple Paths for Nonphysiological Transport of K
+
in
Escherichia coli
Authors: Buurman Ed T. , McLaggan Debbie , Naprstek Josef , Epstein Wolfgang 
Published: June 2004

ABSTRACT

Mutants of
Escherichia coli
lacking all of the known saturable K
+
transport systems, “triple mutants,” require elevated K
+
concentrations for growth. K
+
transport activity in such mutants, called TrkF activity, has low substrate specificity and a low rate that increases with increasing external pH. Attempts to isolate mutants requiring even higher concentrations of K
+
failed, implying that either TrkF is essential or is composed of multiple minor K
+
transport activities. Instead, we sought mutations that allowed triple mutants to grow at lower K
+
concentrations. Mutations so identified include ones altering MscL, the large mechanosensitive channel, or Opp, the oligopeptide permease. However, a possible contribution of wild-type Opp and MscL to TrkF activity was not proven. In contrast, expression of wild-type ProP, TrkG, and TrkH proteins increased uptake when encoded on multicopy plasmids. In all of these situations, the driving force for K
+
appeared to be the transmembrane electric potential, and in most cases substrate specificity was low; these are characteristics of TrkF activity. These results support the view that TrkF is composed of multiple, “aberrant” K
+
transport activities, i.e., paths that, regardless of their physiological function, allow K
+
to cross the cell membrane by a uniport process.
Energetics of Gliding Motility in
Mycoplasma mobile
Authors: Jaffe Jacob D. , Miyata Makoto , Berg Howard C. 
Published: June 2004

ABSTRACT

Mycoplasma mobile
glides on surfaces at up to 7 μm/s by an unknown mechanism. We studied the energetics that power gliding by using a novel, growth medium-free system. We found that cells could glide in defined media if the glass substrate is preconditioned by exposure to horse serum. The active component that potentiates gliding is sensitive to proteinase K treatment. We used the defined medium system to test the effect of various inhibitors, ionophores, and poisons on motility of
M. mobile
. Valinomycin, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP),
N,N
′-dicyclohexylcarbodiimide, phenamil, amiloride, rifampin, and puromycin had no short-term effects on gliding. We also confirmed that we were able to modulate the membrane potential with valinomycin and FCCP by using a potential-sensitive dye. Shifting the pH likewise had no effect on motility. These results rule out the use of conventional ion motive forces to power gliding. Arsenate had a dramatic inhibitory effect on gliding, and both the speed and the fraction of cells moving tracked ATP levels. Sodium orthovanadate had a slight but significant inhibitory effect on gliding. Taken together, these results suggest that the motor system of
M. mobile
is likely an ATPase or is directly coupled to an ATPase.
Autoinduction ofBacillus subtilis phoPROperon Transcription Results from Enhanced Transcription from EσA- and EσE-Responsive Promoters by Phosphorylated PhoP
Authors: Paul Salbi , Birkey Stephanie , Liu Wei , Hulett F. Marion 
Published: June 2004

ABSTRACTThephoPRoperon encodes a response regulator, PhoP, and a histidine kinase, PhoR, which activate or repress genes of theBacillus subtilisPho regulon in response to an extracellular phosphate deficiency. Induction ofphoPRupon phosphate starvation required activity of both PhoP and PhoR, suggesting autoregulation of the operon, a suggestion that is supported here by PhoP footprinting on thephoPRpromoter. Primer extension analyses, using RNA from JH642 or isogenicsigEorsigBmutants isolated at different stages of growth and/or under different growth conditions, suggested that expression of thephoPRoperon represents the sum of five promoters, each responding to a specific growth phase and environmental controls. The temporal expression of thephoPRpromoters was investigated using in vitro transcription assays with RNA polymerase holoenzyme isolated at different stages of Pho induction, from JH642 or isogenicsigEorsigBmutants. In vitro transcription studies using reconstituted EσA, EσB, and EσEholoenzymes identified PA4and PA3as EσApromoters and PE2as an EσEpromoter. Phosphorylated PhoP (PhoP∼P) enhanced transcription from each of these promoters. EσBwas sufficient for in vitro transcription of the PB1promoter. P5was active only in asigBmutant strain. These studies are the first to report a role for PhoP∼P in activation of promoters that also have activity in the absence of Pho regulon induction and an activation role for PhoP∼P at an EσEpromoter. Information concerning PB1and P5creates a basis for further exploration of the regulatory coordination or overlap of the PhoPR and SigB regulons during phosphate starvation.
Vibrio fischeri
Flagellin A Is Essential for Normal Motility and for Symbiotic Competence during Initial Squid Light Organ Colonization
Authors: Millikan Deborah S. , Ruby Edward G. 
Published: June 2004

ABSTRACT

The motile bacterium
Vibrio fischeri
is the specific bacterial symbiont of the Hawaiian squid
Euprymna scolopes
. Because motility is essential for initiating colonization, we have begun to identify stage-specific motility requirements by creating flagellar mutants that have symbiotic defects.
V. fischeri
has six flagellin genes that are uniquely arranged in two chromosomal loci,
flaABCDE
and
flaF
. With the exception of the
flaA
product, the predicted gene products are more similar to each other than to flagellins of other
Vibrio
species. Immunoblot analysis indicated that only five of the six predicted proteins were present in purified flagella, suggesting that one protein, FlaF, is unique with respect to either its regulation or its function. We created mutations in two genes,
flaA
and
flaC
. Compared to a
flaC
mutant, which has wild-type flagellation, a strain having a mutation in the
flaA
gene has fewer flagella per cell and exhibits a 60% decrease in its rate of migration in soft agar. During induction of light organ symbiosis, colonization by the
flaA
mutant is impaired, and this mutant is severely outcompeted when it is presented to the animal as a mixed inoculum with the wild-type strain. Furthermore,
flaA
mutant cells are preferentially expelled from the animal, suggesting either that FlaA plays a role in adhesion or that normal motility is an advantage for retention within the host. Taken together, these results show that the flagellum of
V. fischeri
is a complex structure consisting of multiple flagellin subunits, including FlaA, which is essential both for normal flagellation and for motility, as well as for effective symbiotic colonization.
Displacements of Prohead Protease Genes in the Late Operons of Double-Stranded-DNA Bacteriophages
Authors: Liu Jing , Mushegian Arcady 
Published: June 2004

ABSTRACT
Most of the known prohead maturation proteases in double-stranded-DNA bacteriophages are shown, by computational methods, to fall into two evolutionarily independent clans of serine proteases, herpesvirus assemblin-like and ClpP-like. Phylogenetic analysis suggests that these two types of phage prohead protease genes displaced each other multiple times while preserving their exact location within the late operons of the phage genomes.
Spike Structure at the Interface between GlidingMycoplasma mobileCells and Glass Surfaces Visualized by Rapid-Freeze-and-Fracture Electron Microscopy
Authors: Miyata Makoto , Petersen Jennifer D. 
Published: June 2004

ABSTRACTMycoplasma mobileis a flask-shaped bacteria that binds to a substrate and glides towards its tapered end, the so-called “head-like protrusion,” by an unknown mechanism. To search for cellular structures underlying this motility, the cell-substrate interface of actively gliding cells was visualized by rapid-freeze-and-freeze-fracture rotary-shadow electron microscopy. Novel structures, called “spikes,” were observed to protrude from the cell membrane and attach to the glass surface at their distal end. The spikes were on average 50 nm in length and 4 nm in diameter, most abundant around the head, and not observed in a nonbinding mutant. The spikes may be involved in the mechanism of binding, gliding, or both.
Insulation of the σFRegulatory System inBacillus subtilis
Authors: Carniol Karen , Kim Tae-Jong , Price Chester W. , Losick Richard 
Published: June 2004

ABSTRACTThe transcription factors σFand σBare related RNA polymerase sigma factors that govern dissimilar networks of adaptation to stress conditions inBacillus subtilis. The two factors are controlled by closely related regulatory pathways, involving protein kinases and phosphatases. We report that insulation of the σFpathway from the σBpathway involves the integrated action of both the cognate kinase and the cognate phosphatase.
Independent Regulation of Two Genes in
Escherichia coli
by Tetracyclines and Tet Repressor Variants
Authors: Kamionka Annette , Sehnal Miriam , Scholz Oliver , Hillen Wolfgang 
Published: June 2004

ABSTRACT

We report a regulation system in
Escherichia coli
for independent regulation of two distinct reporter genes by application of Tet repressors with different specificities. One Tet repressor variant comprises wild-type
tet
operator (
tetO
) recognition and exclusive induction with the novel inducer 4-dedimethylamino-anhydrotetracycline. The other Tet repressor variant shows
tetO-
4C recognition and induction with tetracycline. We demonstrate that both variants are independently active in vivo and allow selective regulation of two genes in the same cell without any cross talk.
TheponAGene ofEnterococcus faecalisJH2-2 Codes for a Low-Affinity Class A Penicillin-Binding Protein
Authors: Duez Colette , Hallut Séverine , Rhazi Noureddine , Hubert Séverine , Amoroso Ana , Bouillenne Fabrice , Piette André , Coyette Jacques 
Published: June 2004

ABSTRACTA soluble derivative of theEnterococcus faecalisJH2-2 class A PBP1 (*PBP1) was overproduced and purified. It exhibited a glycosyltransferase activity on theEscherichia coli14C-labeled lipid II precursor. As add-peptidase, it could hydrolyze thiolester substrates with efficiencies similar to those of other class A penicillin-binding proteins (PBPs) and bind β-lactams, but withk2/K(a parameter accounting for the acylation step efficiency) values characteristic of penicillin-resistant PBPs.
Genital condylomata in a patient receiving infliximab for Crohn’s disease
Authors: Somasekar A , Alcolado R 
Published: June 2004

Abstract
Infliximab is a monoclonal antibody against tumour necrosis factor-alpha. Recent studies have shown that it is effective in treating patients with refractory Crohn’s disease and in those with Crohn’s fistulae. Though this drug is found to be safe in clinical trials, sporadic reports of serious complications have been recorded in the literature. The case of a patient who developed profuse genital warts after infliximab treatment is reported. The literature is reviewed and information is presented on side effects and complications as a result of infliximab therapy.
Evolving immunotherapeutic strategies in bladder and renal cancer
Authors: Griffiths T R L , Mellon J K 
Published: June 2004

Abstract
For patients with urological cancers, immunotherapy is currently a treatment option for metastatic renal cell carcinoma, and those with “high risk” superficial bladder cancers. In this review, our current understanding of tumour immune escape is discussed. The principles and role of current immunotherapies for these tumours are described, and new areas of immunotherapeutic promise are highlighted.