bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Positive Regulatory Loop Controls Expression of the Locus of Enterocyte Effacement-Encoded Regulators Ler and GrlA
Authors: Barba Jeannette , Bustamante Víctor H. , Flores-Valdez Mario A. , Deng Wanyin , Finlay B. Brett , Puente José L. 
Published: November 2005

ABSTRACTThe formation of attaching and effacing (A/E) lesions on intestinal epithelial cells is an essential step in the pathogenesis of human enteropathogenic and enterohemorrhagicEscherichia coliand of the mouse pathogenCitrobacter rodentium. The genes required for the development of the A/E phenotype are located within a pathogenicity island known as thelocus ofenterocyteeffacement (LEE). The LEE-encoded transcriptional regulators Ler, an H-NS-like protein, and GrlA, a member of a novel family of transcriptional activators, positively control the expression of the genes located in the LEE and their corresponding virulence. In this study, we usedC. rodentiumas a model to study the mechanisms controlling the expression of Ler and GrlA. By deletion analysis of thelerandgrlRAregulatory regions and complementation experiments, negative and positivecis-acting regulatory motifs were identified that are essential for the regulation of both genes. This analysis confirmed that GrlA is required for the activation ofler, but it also showed that Ler is required for the expression ofgrlRA, revealing a novel regulatory loop controlling the optimal expression of virulence genes in A/E pathogens. Furthermore, our results indicate that Ler and GrlA induce the expression of each other by, at least in part, counteracting the repression mediated by H-NS. However, whereas GrlA is still required for the optimal expression oflereven in the absence of H-NS, Ler is not needed for the expression ofgrlRAin the absence of H-NS. This type of transcriptional positive regulatory loop represents a novel mechanism in pathogenic bacteria that is likely required to maintain an appropriate spatiotemporal transcriptional response during infection.
Identification and Characterization of a Novel Outer Membrane Protein (OMP J) of
Moraxella catarrhalis
That Exists in Two Major Forms
Authors: Hays John P. , van Selm Saskia , Hoogenboezem Theo , Estevão Silvia , Eadie Kimberly , van Veelen Peter , Tommassen Jan , van Belkum Alex , Hermans Peter W. M. 
Published: November 2005

ABSTRACT

Moraxella catarrhalis
is a common commensal of the human respiratory tract that has been associated with a number of disease states, including acute otitis media in children and exacerbations of chronic obstructive pulmonary disease in adults. During studies to investigate the outer membrane proteins of this bacterium, two novel major proteins, of approximately 19 kDa and 16 kDa (named OMP J1 and OMP J2, respectively), were identified. Further analysis indicated that these two proteins possessed almost identical gene sequences, apart from two insertion/deletion events in predicted external loops present within the putative barrel-like structure of the proteins. The development of a PCR screening strategy found a 100% (96/96) incidence for the genes encoding the OMP J1 and OMP J2 proteins within a set of geographically diverse
M. catarrhalis
isolates, as well as a significant association of OMP J1/OMP J2 with both the genetic lineage and the complement resistance phenotype (Fisher's exact test;
P
< 0.01). Experiments using two Δ
ompJ2
mutants (one complement resistant and the other complement sensitive) indicated that both were less easily cleared from the lungs of mice than were their isogenic wild-type counterparts, with a significant difference in bacterial clearance being observed for the complement-resistant isolate but not for its isogenic Δ
ompJ2
mutant (unpaired Student's
t
test;
P
< 0.001 and
P
= 0.32). In this publication, we characterize a novel outer membrane protein of
Moraxella catarrhalis
which exists in two variant forms associated with particular genetic lineages, and both forms are suggested to contribute to bacterial clearance from the lungs.
Molecular Analysis and Organization of the σ
B
Operon in
Staphylococcus aureus
Authors: Senn Maria Magdalena , Giachino Philipp , Homerova Dagmar , Steinhuber Andrea , Strassner Jochen , Kormanec Jan , Flückiger Ursula , Berger-Bächi Brigitte , Bischoff Markus 
Published: November 2005

ABSTRACT

The alternative sigma factor σ
B
of
Staphylococcus aureus
controls the expression of a variety of genes, including virulence determinants and global regulators. Genetic manipulations and transcriptional start point (TSP) analyses showed that the
sigB
operon is transcribed from at least two differentially controlled promoters: a putative σ
A
-dependent promoter, termed
sigB
p1
, giving rise to a 3.6-kb transcript covering sa2059
-
sa2058
-rsbU-rsbV-rsbW-sigB
, and a σ
B
-dependent promoter,
sigB
p3
, initiating a 1.6-kb transcript covering
rsbV-rsbW-sigB
. TSP and promoter-reporter gene fusion experiments indicated that a third promoter, tentatively termed
sigB
p2
and proposed to lead to a 2.5-kb transcript, including
rsbU-rsbV-rsbW-sigB
, might govern the expression of the
sigB
operon. Environmental stresses, such as heat shock and salt stress, induced a rapid response within minutes from promoters
sigB
p1
and
sigB
p3
. In vitro, the
sigB
p1
promoter was active in the early growth stages, while the
sigB
p2
and
sigB
p3
promoters produced transcripts throughout the growth cycle, with
sigB
p3
peaking around the transition state between exponential growth and stationary phase. The amount of
sigB
transcripts, however, did not reflect the concentration of σ
B
measured in cell extracts, which remained constant over the entire growth cycle. In a guinea pig cage model of infection,
sigB
transcripts were as abundant 2 and 8 days postinoculation as values found in vitro, demonstrating that
sigB
is indeed transcribed during the course of infection. Physical interactions between staphylococcal RsbU-RsbV, RsbV-RsbW, and RsbW-σ
B
were inferred from a yeast (
Saccharomyces cerevisiae
) two-hybrid approach, indicating the presence of a partner-switching mechanism in the σ
B
activation cascade similar to that of
Bacillus subtilis
. The finding that overexpression of RsbU was sufficient to trigger an immediate and strong activation of σ
B
, however, signals a relevant difference in the regulation of σ
B
activation between
B. subtilis
and
S. aureus
in the cascade upstream of RsbU.
Comparative Analysis of Two Classes of Quorum-Sensing Signaling Systems That Control Production of Extracellular Proteins and Secondary Metabolites inErwinia carotovoraSubspecies
Authors: Chatterjee Asita , Cui Yaya , Hasegawa Hiroaki , Leigh Nathan , Dixit Vaishali , Chatterjee Arun K. 
Published: November 2005

ABSTRACTInErwinia carotovorasubspecies,N-acyl homoserine lactone (AHL) controls the expression of various traits, including extracellular enzyme/protein production and pathogenicity. We report here thatE. carotovorasubspecies possess two classes of quorum-sensing signaling systems defined by the nature of the major AHL analog produced as well as structural and functional characteristics of AHL synthase (AhlI) and AHL receptor (ExpR). Class I strains represented byE. carotovorasubsp.atrosepticastrain Eca12 andE. carotovorasubsp.carotovorastrains EC153 and SCC3193 produce 3-oxo-C8-HL (N-3-oxooctanoyl-l-homoserine lactone) as the major AHL analog as well as low but detectable levels of 3-oxo-C6-HL (N-3-oxohexanoyl-l-homoserine lactone). In contrast, the members of class II (i.e.,E. carotovorasubsp.betavasculorumstrain Ecb168 andE. carotovorasubsp.carotovorastrains Ecc71 and SCRI193) produce 3-oxo-C6-HL as the major analog. ExpR species of both classes activatersmA(Rsm, repressor of secondary metabolites) transcription and bindrsmADNA. Gel mobility shift assays with maltose-binding protein (MBP)-ExpR71and MBP-ExpR153fusion proteins show that both bind a 20-mer sequence present inrsmA. The two ExpR functions (i.e.,expR-mediated activation ofrsmAexpression and ExpR binding withrsmADNA) are inhibited by AHL. The AHL effects are remarkably specific in thatexpReffect of EC153, a strain belonging to class I, is counteracted by 3-oxo-C8-HL but not by 3-oxo-C6-HL. Conversely, theexpReffect of Ecc71, a strain belonging to class II, is neutralized by 3-oxo-C6-HL but not by 3-oxo-C8-HL. The AHL responses correlated withexpR-mediated inhibition of exoprotein and secondary metabolite production.
Genome-Wide Transcriptional Analysis of the Phosphate Starvation Stimulon ofBacillus subtilis
Authors: Allenby Nicholas E. E. , O'Connor Nicola , Prágai Zoltán , Ward Alan C. , Wipat Anil , Harwood Colin R. 
Published: November 2005

ABSTRACTBacillus subtilisresponds to phosphate starvation stress by inducing the PhoP and SigB regulons. While the PhoP regulon provides a specific response to phosphate starvation stress, maximizing the acquisition of phosphate (Pi) from the environment and reducing the cellular requirement for this essential nutrient, the SigB regulon provides nonspecific resistance to stress by protecting essential cellular components, such as DNA and membranes. We have characterized the phosphate starvation stress response ofB. subtilisat a genome-wide level using DNA macroarrays. A combination of outlier and cluster analyses identified putative new members of the PhoP regulon, namely,yfkN(2′,3′ cyclic nucleotide 2′-phosphodiesterase),yurI(RNase),yjdB(unknown), andvpr(extracellular serine protease). YurI is thought to be responsible for the nonspecific degradation of RNA, while the activity of YfkN on various nucleotide phosphates suggests that it could act on substrates liberated by YurI, which produces 3′ or 5′ phosphoribonucleotides. The putative new PhoP regulon members are either known or predicted to be secreted and are likely to be important for the recovery of inorganic phosphate from a variety of organic sources of phosphate in the environment.
Characterization of Temporal Protein Production in
Pseudomonas aeruginosa
Biofilms
Authors: Southey-Pillig Christopher J. , Davies David G. , Sauer Karin 
Published: November 2005

ABSTRACT

Phenotypic and genetic evidence supporting the notion of biofilm formation as a developmental process is growing. In the present work, we provide additional support for this hypothesis by identifying the onset of accumulation of biofilm-stage specific proteins during
Pseudomonas aeruginosa
biofilm maturation and by tracking the abundance of these proteins in planktonic and three biofilm developmental stages. The onset of protein production was found to correlate with the progression of biofilms in developmental stages. Protein identification revealed that proteins with similar function grouped within similar protein abundance patterns. Metabolic and housekeeping proteins were found to group within a pattern separate from virulence, antibiotic resistance, and quorum-sensing-related proteins. The latter were produced in a progressive manner, indicating that attendant features that are characteristic of biofilms such as antibiotic resistance and virulence may be part of the biofilm developmental process. Mutations in genes for selected proteins from several protein production patterns were made, and the impact of these mutations on biofilm development was evaluated. The proteins cytochrome
c
oxidase, a probable chemotaxis transducer, a two-component response regulator, and MexH were produced only in mature and late-stage biofilms. Mutations in the genes encoding these proteins did not confer defects in growth, initial attachment, early biofilm formation, or twitching motility but were observed to arrest biofilm development at the stage of cell cluster formation we call the maturation-1 stage. The results indicated that expression of theses genes was required for the progression of biofilms into three-dimensional structures on abiotic surfaces and the completion of the biofilm developmental cycle. Reverse transcription-PCR analysis confirmed the detectable change in expression of the respective genes
ccoO
, PA4101, and PA4208. We propose a possible mechanism for the role of these biofilm-specific proteins in biofilm formation.
Isolation and Characterization of New Thiamine-Deregulated Mutants of
Bacillus subtilis
Authors: Schyns Ghislain , Potot Sébastien , Geng Yi , Barbosa Teresa M. , Henriques Adriano , Perkins John B. 
Published: November 2005

ABSTRACT

In bacteria, thiamine pyrophosphate (TPP) is an essential cofactor that is synthesized de novo. Thiamine, however, is not an intermediate in the biosynthetic pathway but is salvaged from the environment and phosphorylated to TPP. We have isolated and characterized new mutants of
Bacillus subtilis
that deregulate thiamine biosynthesis and affect the export of thiamine products from the cell. Deletion of the
ydiA
gene, which shows significant similarity to the thiamine monophosphate kinase gene of
Escherichia coli
(
thiL
), did not generate the expected thiamine auxotroph but instead generated a thiamine bradytroph that grew to near-wild-type levels on minimal medium. From this Δ
thiL
deletion mutant, two additional ethyl methanesulfonate-induced mutants that derepressed the expression of a
thiC-lacZ
transcriptional reporter were isolated. One mutant, Tx1, contained a nonsense mutation within the
B. subtilis yloS
(
thiN
) gene that encodes a thiamine pyrophosphokinase, a result which confirmed that
B. subtilis
contains a single-step, yeast-like thiamine-to-TPP pathway in addition to the bacterial TPP de novo pathway. A second mutant, strain Tx26, was shown to contain two lesions. Genetic mapping and DNA sequencing indicated that the first mutation affected
yuaJ
, which encodes a thiamine permease. The second mutation was located within the
ykoD
cistron of the
ykoFEDC
operon, which putatively encodes the ATPase component of a unique thiamine-related ABC transporter. Genetic and microarray studies indicated that both the mutant
yuaJ
and
ykoD
genes were required for the derepression of thiamine-regulated genes. Moreover, the combination of the four mutations (the Δ
thiL
,
thiN
,
yuaJ
, and
ykoD
mutations) into a single strain significantly increased the production and excretion of thiamine products into the culture medium. These results are consistent with the proposed “riboswitch” mechanism of thiamine gene regulation (W. C. Winkler, A. Nahvi, and R. R. Breaker, Nature
419:
952-956, 2002).
Homodimeric Hexaprenyl Pyrophosphate Synthase from the Thermoacidophilic Crenarchaeon
Sulfolobus solfataricus
Displays Asymmetric Subunit Structures
Authors: Sun Han-Yu , Ko Tzu-Ping , Kuo Chih-Jung , Guo Rey-Ting , Chou Chia-Cheng , Liang Po-Huang , Wang Andrew H.-J. 
Published: November 2005

ABSTRACT

Hexaprenyl pyrophosphate synthase (HexPPs) from
Sulfolobus solfataricus
catalyzes the synthesis of
trans
-C
30
-hexaprenyl pyrophosphate (HexPP) by reacting two isopentenyl pyrophosphate molecules with one geranylgeranyl pyrophosphate. The crystal structure of the homodimeric C
30
-HexPPs resembles those of other
trans
-prenyltransferases, including farnesyl pyrophosphate synthase (FPPs) and octaprenyl pyrophosphate synthase (OPPs). In both subunits, 10 core helices are arranged about a central active site cavity. Leu164 in the middle of the cavity controls the product chain length. Two protein conformers are observed in the
S. solfataricus
HexPPs structure, and the major difference between them occurs in the flexible region of residues 84 to 100. Several helices (αI, αJ, αK, and part of αH) and the associated loops have high-temperature factors in one monomer, which may be related to the domain motion that controls the entrance to the active site. Different side chain conformations of Trp136 in two HexPPs subunits result in weaker hydrophobic interactions at the dimer interface, in contrast to the symmetric π-π stacking interactions of aromatic side chains found in FPPs and OPPs. Finally, the three-conformer switched model may explain the catalytic process for HexPPs.
A Degenerate Type III Secretion System from Septicemic
Escherichia coli
Contributes to Pathogenesis
Authors: Ideses Diana , Gophna Uri , Paitan Yossi , Chaudhuri Roy R. , Pallen Mark J. , Ron Eliora Z. 
Published: November 2005

ABSTRACT

The type III secretion system (T3SS) is an important virulence factor used by several gram-negative bacteria to deliver effector proteins which subvert host cellular processes. Enterohemorrhagic
Escherichia coli
O157 has a well-defined T3SS involved in attachment and effacement (ETT1) and critical for virulence. A gene cluster potentially encoding an additional T3SS (ETT2), which resembles the SPI-1 system in
Salmonella enterica
, was found in its genome sequence. The ETT2 gene cluster has since been found in many
E. coli
strains, but its in vivo role is not known. Many of the ETT2 gene clusters carry mutations and deletions, raising the possibility that they are not functional. Here we show the existence in septicemic
E. coli
strains of an ETT2 gene cluster, ETT2
sepsis
, which, although degenerate, contributes to pathogenesis. ETT2
sepsis
has several premature stop codons and a large (5 kb) deletion, which is conserved in 11
E. coli
strains from cases of septicemia and newborn meningitis. A null mutant constructed to remove genes coding for the putative inner membrane ring of the secretion complex exhibited significantly reduced virulence. These results are the first demonstration of the importance of ETT2 for pathogenesis.
Four Unusual Two-Component Signal Transduction Homologs, RedC to RedF, Are Necessary for Timely Development inMyxococcus xanthus
Authors: Higgs Penelope I. , Cho Kyungyun , Whitworth David E. , Evans Lisa S. , Zusman David R. 
Published: November 2005

ABSTRACTWe identified a cluster of four two-component signal transduction genes that are necessary for proper progression ofMyxococcus xanthusthrough development.redCtoredFmutants developed and sporulated early, resulting in small, numerous, and disorganized fruiting bodies. Yeast two-hybrid analyses suggest that RedCDEF act in a single signaling pathway. The previously identifiedespAgene displays a phenotype similar to that ofredCDEF. However, combined mutants defective inespA redCDEFexhibited a striking additive developmental phenotype, suggesting that EspA and RedC to RedF play independent roles in controlling developmental progression.
Vancomycin Stress Response in a Sensitive and a Tolerant Strain ofStreptococcus pneumoniae
Authors: Haas Wolfgang , Kaushal Deepak , Sublett Jack , Obert Caroline , Tuomanen Elaine I. 
Published: November 2005

ABSTRACTThe vancomycin stress response was studied inStreptococcus pneumoniaestrains T4 (TIGR4) and Tupelo. Vancomycin affected the expression of 175 genes, including genes encoding transport functions and enzymes involved in aminosugar metabolism. The two-component systems TCS03, TCS11, and CiaRH also responded to antibiotic treatment. We hypothesize that the three regulons are an important part of the bacterium's response to vancomycin stress.
Iron-Responsive Regulation of Biofilm Formation in
Staphylococcus aureus
Involves Fur-Dependent and Fur-Independent Mechanisms
Authors: Johnson Miranda , Cockayne Alan , Williams Peter H. , Morrissey Julie A. 
Published: November 2005

ABSTRACT

We have shown that
Staphylococcus aureus
biofilm production is induced in iron-restricted conditions and is repressed by iron via a Fur-independent mechanism, while Fur has both positive and negative regulatory roles in low iron. Furthermore, there is no significant increase in polymeric
N
-acetylglucosamine polysaccharide expression to account for induction of biofilms in low iron.
Expectations and Equilibrium in High-Grade Australian Bond Markets
Authors: In Francis , Batten Jonathan A. 
Published: November 2005

This paper examines the equilibrium implications of the Expectations Hypothesis of term structure to different maturities of high-grade Australian dollar denominated Eurobonds and Australian Government bonds (AGBs) using the Canonical Cointegrating Regression (CCR) technique developed by Econometrica 60 (1992) 119. Our findings provide evidence only for equilibrium relationships between each group of bonds based on credit class, but not between any of the subsets of AGBs and the Eurobonds. Furthermore, the error correction model supports theory with the most liquid, long-term 10-year AGB driving the AGB term structure, with short-term yields adjusting to movements in the long-run yields, though the opposite is true for Eurobonds. The lesson for markets is to simplify the risk management task. Managers are advised to treat portfolios of equivalent credit class separately for hedging and risk management.
A preliminary step towards a language for picture control in a real-time mode
Authors: Katz Lou , Etra Bill 
Published: November 2005

With the proliferation of extremely complex analog systems for the control of television images it has become evident that some more efficient system has to be found for dealing with the mire of knobs, switches, levers, and patch cords which make up any video processing device. In planning an attack on this situation, we soon realized that a major aspect of the problem is a linquistic one. Television has only a few terms which deal with the almost infinite number of effects possible in any given system. The specification of wipes, fades, dissolves, keys, etc. tells one the process used, but does not go into great detail as to what it looks like on the screen. A circle wipe, for instance, may start in any part of the screen, have an edge in any of several degrees of softness, may be modulated by a wide range of frequencies, and may have a number of outlines around it in any combination of colors. Given these technical capabilities, the problem of how to catalog the possible effects and how to specify them was approached in terms of a description based on a Cartesian coordinate system representation of the multidimensional video space.
The use of such a coordinate system has given us several advantages. The first is that there is a large body of existing work dealing with physical movements along orthogonal axes. Secondly, image color in television can be measured or specified in terms of phase shifts from 0 to 360 degrees in a planar reference axis system. Another consideration which makes this description natural is that it is standard for zero voltage on a CRT display to be center screen, thus defining our origin and relating it in a simple way to the physical control values. With this as our point of departure we embarked on our work with the clear realization that, because the dimensions and variability of the system were almost infinite, due to the unconstrained combination of analog patches and digital programming, some severe restraint would be necessary in order to make the results meaningful.
Control structures for performance graphics
Authors: DeFanti T. A. , Sandin D. J. , Ainsworth R. A. 
Published: November 2005

Responsive control structures allow graphics systems to be used as performance instruments. Control structures are a design element of a system—while they are manipulated by the user or performer, they exist primarily as a result of the system designer's software and hardware engineering.
For example, the control structure of the telephone system allows ten sequential inputs to connect your phone to almost any other in the world. The power of this structure is independent of the specific user control device. Dials, push buttons, tones and clicks can all be used as inputs.
While physical controls provide inputs, control structures determine what these inputs do.