bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Two Homologous Disulfide Bond Systems Involved in Virulence Factor Biogenesis in Uropathogenic
Escherichia coli
CFT073
Authors: Totsika Makrina , Heras Begoña , Wurpel Daniël J. , Schembri Mark A. 
Published: April 2009

ABSTRACT

D
i
s
ulfide
b
ond (DSB) formation is catalyzed by disulfide bond proteins and is critical for the proper folding and functioning of secreted and membrane-associated bacterial proteins. Uropathogenic
Escherichia coli
(UPEC) strains possess two paralogous disulfide bond systems: the well-characterized DsbAB system and the recently described DsbLI system. In the DsbAB system, the highly oxidizing DsbA protein introduces disulfide bonds into unfolded polypeptides by donating its redox-active disulfide and is in turn reoxidized by DsbB. DsbA has broad substrate specificity and reacts readily with reduced unfolded proteins entering the periplasm. The DsbLI system also comprises a functional redox pair; however, DsbL catalyzes the specific oxidative folding of the large periplasmic enzyme arylsulfate sulfotransferase (ASST). In this study, we characterized the DsbLI system of the prototypic UPEC strain CFT073 and examined the contributions of the DsbAB and DsbLI systems to the production of functional flagella as well as type 1 and P fimbriae. The DsbLI system was able to catalyze disulfide bond formation in several well-defined DsbA targets when provided in
trans
on a multicopy plasmid. In a mouse urinary tract infection model, the isogenic
dsbAB
deletion mutant of CFT073 was severely attenuated, while deletion of
dsbLI
or
assT
did not affect colonization.
Quorum-Sensing Control of Antibiotic Synthesis in
Burkholderia thailandensis
Authors: Duerkop Breck A. , Varga John , Chandler Josephine R. , Peterson Snow Brook , Herman Jake P. , Churchill Mair E. A. , Parsek Matthew R. , Nierman William C. , Greenberg E. Peter 
Published: April 2009

ABSTRACT

The genome of
Burkholderia thailandensis
codes for several LuxR-LuxI quorum-sensing systems. We used
B. thailandensis
quorum-sensing deletion mutants and recombinant
Escherichia coli
to determine the nature of the signals produced by one of the systems, BtaR2-BtaI2, and to show that this system controls genes required for the synthesis of an antibiotic. BtaI2 is an acyl-homoserine lactone (acyl-HSL) synthase that produces two hydroxylated acyl-HSLs,
N
-3-hydroxy-decanoyl-HSL (3OHC
10
-HSL) and
N
-3-hydroxy-octanoyl-HSL (3OHC
8
-HSL). The
btaI2
gene is positively regulated by BtaR2 in response to either 3OHC
10
-HSL or 3OHC
8
-HSL. The
btaR2-btaI2
genes are located within clusters of genes with annotations that suggest they are involved in the synthesis of polyketide or peptide antibiotics. Stationary-phase cultures of wild-type
B. thailandensis
, but not a
btaR2
mutant or a strain deficient in acyl-HSL synthesis, produced an antibiotic effective against gram-positive bacteria. Two of the putative antibiotic synthesis gene clusters require BtaR2 and either 3OHC
10
-HSL or 3OHC
8
-HSL for activation. This represents another example where antibiotic synthesis is controlled by quorum sensing, and it has implications for the evolutionary divergence of
B. thailandensis
and its close relatives
Burkholderia pseudomallei
and
Burkholderia mallei
.
Inhibition of Transcription inStaphylococcus aureusby a Primary Sigma Factor-Binding Polypeptide from Phage G1
Authors: Dehbi Mohammed , Moeck Gregory , Arhin Francis F. , Bauda Pascale , Bergeron Dominique , Kwan Tony , Liu Jing , McCarty John , DuBow Michael , Pelletier Jerry 
Published: April 2009

ABSTRACTThe primary sigma factor ofStaphylococcus aureus, σSA, regulates the transcription of many genes, including several essential genes, in this bacterium via specific recognition of exponential growth phase promoters. In this study, we report the existence of a novel staphylococcal phage G1-derived growth inhibitory polypeptide, referred to as G1ORF67, that interacts with σSAboth in vivo and in vitro and regulates its activity. Delineation of the minimal domain of σSAthat is required for its interaction with G1ORF67 as amino acids 294 to 360 near the carboxy terminus suggests that the G1 phage-encoded anti-σ factor may occlude the −35 element recognition domain of σSA. As would be predicted by this hypothesis, the G1ORF67 polypeptide abolished both RNA polymerase core-dependent binding of σSAto DNA and σSA-dependent transcription in vitro. While G1ORF67 profoundly inhibits transcription when expressed inS. aureuscells in mode of action studies, our finding that G1ORF67 was unable to inhibit transcription when expressed inEscherichia coliconcurs with its inability to inhibit transcription by theE. coliholoenzyme in vitro. These features demonstrate the selectivity of G1ORF67 forS. aureusRNA polymerase. We predict that G1ORF67 is one of the central polypeptides in the phage G1 strategy to appropriate host RNA polymerase and redirect it to phage reproduction.
The Functional Role of a Conserved Loop in EAL Domain-Based Cyclic di-GMP-Specific Phosphodiesterase
Authors: Rao Feng , Qi Yaning , Chong Hui Shan , Kotaka Masayo , Li Bin , Li Jinming , Lescar Julien , Tang Kai , Liang Zhao-Xun 
Published: April 2009

ABSTRACTEAL domain-based cyclic di-GMP (c-di-GMP)-specific phosphodiesterases play important roles in bacteria by regulating the cellular concentration of the dinucleotide messenger c-di-GMP. EAL domains belong to a family of (β/α)8barrel fold enzymes that contain a functional active site loop (loop 6) for substrate binding and catalysis. By examining the two EAL domain-containing proteins RocR and PA2567 fromPseudomonas aeruginosa, we found that the catalytic activity of the EAL domains was significantly altered by mutations in the loop 6 region. The impact of the mutations ranges from apparent substrate inhibition to alteration of oligomeric structure. Moreover, we found that the catalytic activity of RocR was affected by mutating the putative phosphorylation site (D56N) in the phosphoreceiver domain, with the mutant exhibiting a significantly smaller Michealis constant (Km) than that of the wild-type RocR. Hydrogen-deuterium exchange by mass spectrometry revealed that the decrease inKmcorrelates with a change of solvent accessibility in the loop 6 region. We further examinedAcetobacter xylinusdiguanylate cyclase 2, which is one of the proteins that contains a catalytically incompetent EAL domain with a highly degenerate loop 6. We demonstrated that the catalytic activity of the stand-alone EAL domain toward c-di-GMP could be recovered by restoring loop 6. On the basis of these observations and in conjunction with the structural data of two EAL domains, we proposed that loop 6 not only mediates the dimerization of EAL domain but also controls c-di-GMP and Mg2+ion binding. Importantly, sequence analysis of the 5,862 EAL domains in the bacterial genomes revealed that about half of the EAL domains harbor a degenerate loop 6, indicating that the mutations in loop 6 may represent a divergence of function for EAL domains during evolution.
A Unique Group I Intron in
Coxiella burnetii
Is a Natural Splice Mutant
Authors: Raghavan Rahul , Hicks Linda D. , Minnick Michael F. 
Published: April 2009

ABSTRACT

Cbu.L1917, a group I intron present in the 23S rRNA gene of
Coxiella burnetii
, possesses a unique 3′-terminal adenine in place of a conserved guanine. Here, we show that, unlike all other group I introns, Cbu.L1917 utilizes a different cofactor for each splicing step and has a decreased self-splicing rate in vitro.
The
N
-Acetylmannosamine Transferase Catalyzes the First Committed Step of Teichoic Acid Assembly in
Bacillus subtilis
and
Staphylococcus aureus
Authors: D'Elia Michael A. , Henderson James A. , Beveridge Terry J. , Heinrichs David E. , Brown Eric D. 
Published: April 2009

ABSTRACT

There have been considerable strides made in the characterization of the dispensability of teichoic acid biosynthesis genes in recent years. A notable omission thus far has been an early gene in teichoic acid synthesis encoding the
N
-acetylmannosamine transferase (
tagA
in
Bacillus subtilis
;
tarA
in
Staphylococcus aureus
), which adds
N
-acetylmannosamine to complete the synthesis of undecaprenol pyrophosphate-linked disaccharide. Here, we show that the
N
-acetylmannosamine transferases are dispensable for growth in vitro, making this biosynthetic enzyme the last dispensable gene in the pathway, suggesting that
tagA
(or
tarA
) encodes the first committed step in wall teichoic acid synthesis.
Recruitment of the ParG Segregation Protein to Different Affinity DNA Sites
Authors: Zampini Massimiliano , Derome Andrew , Bailey Simon E. S. , Barillà Daniela , Hayes Finbarr 
Published: April 2009

ABSTRACTThe segrosome is the nucleoprotein complex that mediates accurate plasmid segregation. In addition to its multifunctional role in segrosome assembly, the ParG protein of multiresistance plasmid TP228 is a transcriptional repressor of theparFGpartition genes. ParG is a homodimeric DNA binding protein, with C-terminal regions that interlock into a ribbon-helix-helix fold. Antiparallel β-strands in this fold are presumed to insert into the OFoperator major groove to exert transcriptional control as established for other ribbon-helix-helix factors. The OFlocus comprises eight degenerate tetramer boxes arranged in a combination of direct and inverted orientation. Each tetramer motif likely recruits one ParG dimer, implying that the fully bound operator is cooperatively coated by up to eight dimers. OFwas subdivided experimentally into four overlapping 20-bp sites (A to D), each of which comprises two tetramer boxes separated by AT-rich spacers. Extensive interaction studies demonstrated that sites A to D individually are bound with different affinities by ParG (C > A ≈ B ≫ D). Moreover, comprehensive scanning mutagenesis revealed the contribution of each position in the site core and flanking sequences to ParG binding. Natural variations in the tetramer box motifs and in the interbox spacers, as well as in flanking sequences, each influence ParG binding. The OFoperator apparently has evolved with sites that bind ParG dissimilarly to produce a nucleoprotein complex fine-tuned for optimal interaction with the transcription machinery. The association of other ribbon-helix-helix proteins with complex recognition sites similarly may be modulated by natural sequence variations between subsites.
Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple
Staphylococcus aureus
Genomes Identify Novel Antimicrobial Drug Targets
Authors: Lee Deok-Sun , Burd Henry , Liu Jiangxia , Almaas Eivind , Wiest Olaf , Barabási Albert-László , Oltvai Zoltán N. , Kapatral Vinayak 
Published: April 2009

ABSTRACT

Mortality due to multidrug-resistant
Staphylococcus aureus
infection is predicted to surpass that of human immunodeficiency virus/AIDS in the United States. Despite the various treatment options for
S. aureus
infections, it remains a major hospital- and community-acquired opportunistic pathogen. With the emergence of multidrug-resistant
S. aureus
strains, there is an urgent need for the discovery of new antimicrobial drug targets in the organism. To this end, we reconstructed the metabolic networks of multidrug-resistant
S. aureus
strains using genome annotation, functional-pathway analysis, and comparative genomic approaches, followed by flux balance analysis-based in silico single and double gene deletion experiments. We identified 70 single enzymes and 54 pairs of enzymes whose corresponding metabolic reactions are predicted to be unconditionally essential for growth. Of these, 44 single enzymes and 10 enzyme pairs proved to be common to all 13
S. aureus
strains, including many that had not been previously identified as being essential for growth by gene deletion experiments in
S. aureus
. We thus conclude that metabolic reconstruction and in silico analyses of multiple strains of the same bacterial species provide a novel approach for potential antibiotic target identification.
Mutations in Flk, FlgG, FlhA, and FlhE That Affect the Flagellar Type III Secretion Specificity Switch in
Salmonella enterica
Authors: Hirano Takanori , Mizuno Shino , Aizawa Shin-Ichi , Hughes Kelly T. 
Published: April 2009

ABSTRACT

Upon completion of the flagellar hook-basal body (HBB) structure, the flagellar type III secretion system switches from secreting rod/hook-type to filament-type substrates. The secretion specificity switch has been reported to occur prematurely (prior to HBB completion) in
flk
-null mutants (P. Aldridge, J. E. Karlinsey, E. Becker, F. F. Chevance, and K. T. Hughes, Mol. Microbiol. 60:630-643, 2006) and in distal rod gene gain-of-function mutants (
flgG
* mutants) that produce filamentous rod structures (F. F. Chevance, N. Takahashi, J. E. Karlinsey, J. Gnerer, T. Hirano, R. Samudrala, S. Aizawa, and K. T. Hughes, Genes Dev.
21:
2326-2335, 2007). A fusion of β-lactamase (Bla) to the C terminus of the filament-type secretion substrate FlgM was used to select for mutants that would secrete FlgM-Bla into the periplasmic space and show ampicillin resistance (Ap
r
). Ap
r
resulted from null mutations in the
flhE
gene, C-terminal truncation mutations in the
flhA
gene, null and dominant mutations in the
flk
gene, and
flgG
* mutations. All mutant classes required the hook length control protein (FliK) and the rod cap protein (FlgJ) for the secretion specificity switch to occur. However, neither the hook (FlgE) nor the hook cap (FlgD) protein was required for premature FlgM-Bla secretion in the
flgG
* and
flk
mutant strains, but it was in the
flhE
mutants. Unexpectedly, when deletions of either
flgE
or
flgD
were introduced into
flgG
* mutant strains, filaments were able to grow directly on the filamentous rod structures.
Functional Characterization of Excision Repair and RecA-Dependent Recombinational DNA Repair in
Campylobacter jejuni
Authors: Gaasbeek Esther J. , van der Wal Fimme J. , van Putten Jos P. M. , de Boer Paulo , van der Graaf-van Bloois Linda , de Boer Albert G. , Vermaning Bart J. , Wagenaar Jaap A. 
Published: April 2009

ABSTRACT

The presence and functionality of DNA repair mechanisms in
Campylobacter jejuni
are largely unknown. In silico analysis of the complete translated genome of
C. jejuni
NCTC 11168 suggests the presence of genes involved in methyl-directed mismatch repair (MMR), nucleotide excision repair, base excision repair (BER), and recombinational repair. To assess the functionality of these putative repair mechanisms in
C. jejuni
,
mutS
,
uvrB
,
ung
, and
recA
knockout mutants were constructed and analyzed for their ability to repair spontaneous point mutations, UV irradiation-induced DNA damage, and nicked DNA. Inactivation of the different putative DNA repair genes did not alter the spontaneous mutation frequency. Disruption of the UvrB and RecA orthologues, but not the putative MutS or Ung proteins, resulted in a significant reduction in viability after exposure to UV irradiation. Assays performed with uracil-containing plasmid DNA showed that the putative uracil-DNA glycosylase (Ung) protein, important for initiation of the BER pathway, is also functional in
C. jejuni
. Inactivation of
recA
also resulted in a loss of natural transformation. Overall, the data indicate that
C. jejuni
has multiple functional DNA repair systems that may protect against DNA damage and limit the generation of genetic diversity. On the other hand, the apparent absence of a functional MMR pathway may enhance the frequency of on-and-off switching of phase variable genes typical for
C. jejuni
and may contribute to the genetic heterogeneity of the
C. jejuni
population.
Physicochemical study of complexation and ion-exchange properties of 2-hydroxy-4-ethoxypropiophenone—ethylene glycol polymer
Authors: Patel Jayesh R , Sutaria Dipan H , Patel Magan N 
Published: April 2009

Copolymers (HEPP-EG) were synthesized by the condensation of 2-hydroxy-4-ethoxypropiophenone with ethylene glycol in presence of polyphosphoric acid as a catalyst. The copolymers were characterized by elemental analyses, IR spectra, viscosity and thermal studies. The number-average molecular weight (Mn) was measured by non-aqueous conductometric titration. The copolymer HEPP-EG-6 was complexed with metal ions, Cu2+, Ni2+, Co2, Mn2+ and Zn2+ and characterized. Chelation ion-exchange properties have been studied by employing the batch equilibration method.
T lymphocytes coexpressing CCR4 and a chimeric antigen receptor targeting CD30 have improved homing and antitumor activity in a Hodgkin tumor model
Authors: Di Stasi Antonio , De Angelis Biagio , Rooney Cliona M. , Zhang Lan , Mahendravada Aruna , Foster Aaron E. , Heslop Helen E. , Brenner Malcolm K. , Dotti Gianpietro , Savoldo Barbara 
Published: April 2009

AbstractFor the adoptive transfer of tumor-directed T lymphocytes to prove effective, there will probably need to be a match between the chemokines the tumor produces and the chemokine receptors the effector T cells express. The Reed-Stemberg cells of Hodgkin lymphoma (HL) predominantly produce thymus- and activation-regulated chemokine/CC chemokine ligand 17 (TARC/CCL17) and macrophage-derived chemokine (MDC/CCL22), which preferentially attract type 2 T helper (Th2) cells and regulatory T cells (Tregs) that express the TARC/MDC-specific chemokine receptor CCR4, thus generating an immunosuppressed tumor environment. By contrast, effector CD8+ T cells lack CCR4, are nonresponsive to these chemokines and are rarely detected at the tumor site. We now show that forced expression of CCR4 by effector T cells enhances their migration to HL cells. Furthermore, T lymphocytes expressing both CCR4 and a chimeric antigen receptor directed to the HL associated antigen CD30 sustain their cytotoxic function and cytokine secretion in vitro, and produce enhanced tumor control when infused intravenously in mice engrafted with human HL. This approach may be of value in patients affected by HL.
Penetrating abdominal injuries: management controversies
Authors: Butt Muhammad U , Zacharias Nikolaos , Velmahos George C 
Published: April 2009

Abstract
Penetrating abdominal injuries have been traditionally managed by routine laparotomy. New understanding of trajectories, potential for organ injury, and correlation with advanced radiographic imaging has allowed a shift towards non-operative management of appropriate cases. Although a selective approach has been established for stab wounds, the management of abdominal gunshot wounds remains a matter of controversy. In this chapter we describe the rationale and methodology of selecting patients for non-operative management. We also discuss additional controversial issues, as related to antibiotic prophylaxis, management of asymptomatic thoracoabdominal injuries, and the use of colostomy vs. primary repair for colon injuries.
Accelerated Formation of β-Dicalcium Silicate by Solid-state Reaction in Water Vapor Atmosphere
Authors: Kozawa Takahiro , Onda Ayumu , Yanagisawa Kazumichi 
Published: April 2009

Abstract
β-Ca2SiO4 powders were prepared from commercially available raw materials, CaCO3 and amorphous SiO2 (a-SiO2), by solid-state reactions in water vapor atmosphere. The formation of β-Ca2SiO4 was accelerated by water vapor. Water vapor is considered to enhance the thermal decomposition of CaCO3 and to attack surface Si–O–Si bonds in a-SiO2 to accelerate the formation of β-Ca2SiO4. The effect of water vapor atmosphere on the formation of β-Ca2SiO4 from a mixture of CaCO3 and a-SiO2 was stronger than that of mechanochemical processing for 30 min.
Shape-controlled Preparation of Gold Nanocrystals Using a Microwave–polyol Method
Authors: Tsuji Masaharu , Ueyama Daisuke , Alam Md Jahangir , Hikino Sachie 
Published: April 2009

Abstract
Gold nanocrystals were prepared by a microwave (MW)–polyol method using di-, tetra-, and poly(ethylene glycol)s. When these polyols were heated to 240 °C at a heating rate of 160 °C/min and held at 240 °C for 5 min, icosahedral particles with average diameters of 55–85 nm were prepared from HAuCl4/PVP in di-, tetra- and poly(ethylene glycol)s at high yield (≥91%). Plate-like and decahedral particles were obtained at high yields from HAuCl4/PVP/NaCl.
Crystal Growth of Glycine Controlled by a Focused CW Near-infrared Laser Beam
Authors: Sugiyama Teruki , Adachi Takuji , Masuhara Hiroshi 
Published: April 2009

Abstract
Crystal growth of glycine was accelerated just by focusing a CW 1064-nm laser beam at a position adjacent to a spontaneously generated glycine crystal in D2O. Its rate depended on the distance between the crystal and the focal spot. Interesting crystal growth and dissolution were found, which is considered to be due to Ostwald ripening.
Enantioselective Construction of a 2,8-Dioxabicyclo[3.2.1]octane Ring System via [2,3]-Sigmatropic Rearrangement of Oxonium Ylide Using Chiral Dirhodium(II) Carboxylates
Authors: Shimada Naoyuki , Nakamura Seiichi , Anada Masahiro , Shiro Motoo , Hashimoto Shunichi 
Published: April 2009

Abstract
Dirhodium(II) tetrakis[N-tetrafluorophthaloyl-(S)-tert-leucinate], Rh2(S-TFPTTL)4, is an exceptionally efficient catalyst for enantioselective tandem cyclic oxonium ylide formation and [2,3]-sigmatropic rearrangement from α-diazo-β-ketoester bearing cyclic allylic acetal functionality, providing the 2,8-dioxabicyclo[3.2.1]octane core structure of zaragozic acids in up to 93% ee.
Structures and Dielectric Properties in Thermochromic Nickel(II) Compounds
Authors: Hayami Shinya , Urakami Daisuke , Sato Shoya , Kojima Yoshihiro , Inoue Katsuya , Ohba Masaaki 
Published: April 2009

Abstract
Hysteretic dielectric responses of thermochromic compounds, [Ni(dieten)2]X2 (dieten = N,N-diethylethylenediamine, X− = BF4− and ClO4−) have been observed and discussed based on their structures in low- and high-temperature phases.
Organic Films Containing Trinuclear Ruthenium Clusters that Exhibit Redox-state-dependent Heat-shielding Characteristics
Authors: Tomiyasu Yuki , Abe Masaaki , Morihara Yasushi , Ohgi Hiroyuki , Otake Tomiaki , Hisaeda Yoshio 
Published: April 2009

Abstract
We report here an unprecedented utility of redox-active transition-metal complexes as heat-shielding materials. A poly(vinyl alcohol) film containing mixed-valent cluster [Ru3(μ3-O)(μ-CH3CO2)6(mbpy+)3](PF6)3 (1) (mbpy+ = 1-methyl-4,4′-bipyridinium cation), which strongly absorbs light in the near-infrared region, shows heat-shielding characteristics whose efficiency is found to highly depend on the redox state of the cluster dye.
Interaction of Self-assembled Cationic Nanogels with Oligo-DNA and Function as Artificial Nucleic Acid Chaperone
Authors: Morimoto Nobuyuki , Tamada Junko , Sawada Shin-ichi , Shimada Naohiko , Kano Arihiro , Maruyama Atsushi , Akiyoshi Kazunari 
Published: April 2009

Abstract
Cationic self-assembled nanogels with ethylenediamine or dipropylenetriamine groups formed complex nanoparticles with double-stranded oligo-DNA and accelerated the rate of strand exchange reaction as artificial nucleic acid chaperones.