bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptosporidium parvum
Long-Chain Fatty Acid Elongase
Authors: Fritzler Jason M. , Millership Jason J. , Zhu Guan 
Published: September 2007

ABSTRACT

We report the presence of a new fatty acyl coenzyme A (acyl-CoA) elongation system in
Cryptosporidium
and the functional characterization of the key enzyme, a single long-chain fatty acid elongase (LCE), in this parasite. This enzyme contains conserved motifs and predicted transmembrane domains characteristic to the elongase family and is placed within the ELO6 family specific for saturated substrates. Cp
LCE1
gene transcripts are present at all life cycle stages, but the levels are highest in free sporozoites and in stages at 36 h and 60 h postinfection that typically contain free merozoites. Immunostaining revealed localization to the outer surface of sporozoites and to the parasitophorous vacuolar membrane. Recombinant CpLCE1 displayed allosteric kinetics towards malonyl-CoA and palmitoyl-CoA and Michaelis-Menten kinetics towards NADPH. Myristoyl-CoA (C
14:0
) and palmitoyl-CoA (C
16:0
) display the highest activity when used as substrates, and only one round of elongation occurs. CpLCE1 is fairly resistant to cerulenin, an inhibitor for both type I and II fatty acid synthases (i.e., maximum inhibitions of 20.5% and 32.7% were observed when C
16:0
and C
14:0
were used as substrates, respectively). These observations ultimately validate the function of CpLCE1.
New Insights into the WalK/WalR (YycG/YycF) Essential Signal Transduction Pathway Reveal a Major Role in Controlling Cell Wall Metabolism and Biofilm Formation inStaphylococcus aureus
Authors: Dubrac Sarah , Boneca Ivo Gomperts , Poupel Olivier , Msadek Tarek 
Published: September 2007

ABSTRACTThe highly conserved WalK/WalR (also known as YycG/YycF) two-component system is specific to low-G+C gram-positive bacteria. While this system is essential for cell viability, both the nature of its regulon and its physiological role have remained mostly uncharacterized. We observed that, unexpectedly,Staphylococcus aureuscell death induced by WalKR depletion was not followed by lysis. We show that WalKR positively controls autolytic activity, in particular that of the two majorS. aureusautolysins, AtlA and LytM. By using our previously characterized consensus WalR binding site and carefully reexamining the genome annotations, we identified nine genes potentially belonging to the WalKR regulon that appeared to be involved inS. aureuscell wall degradation. Expression of all of these genes was positively controlled by WalKR levels in the cell, leading to high resistance to Triton X-100-induced lysis when the cells were starved for WalKR. Cells lacking WalKR were also more resistant to lysostaphin-induced lysis, suggesting modifications in cell wall structure. Indeed, lowered levels of WalKR led to a significant decrease in peptidoglycan biosynthesis and turnover and to cell wall modifications, which included increased peptidoglycan cross-linking and glycan chain length. We also demonstrated a direct relationship between WalKR levels and the ability to form biofilms. This is the first example inS. aureusof a regulatory system positively controlling autolysin synthesis and biofilm formation. Taken together, our results now define this signal transduction pathway as a master regulatory system for cell wall metabolism, which we have accordingly renamed WalK/WalR to reflect its true function.
Genome Sequence Analysis of the Emerging Human Pathogenic Acetic Acid Bacterium
Granulibacter bethesdensis
Authors: Greenberg David E. , Porcella Stephen F. , Zelazny Adrian M. , Virtaneva Kimmo , Sturdevant Dan E. , Kupko John J. , Barbian Kent D. , Babar Amenah , Dorward David W. , Holland Steven M. 
Published: September 2007

ABSTRACT

Chronic granulomatous disease (CGD) is an inherited immune deficiency characterized by increased susceptibility to infection with
Staphylococcus
, certain gram-negative bacteria, and fungi.
Granulibacter bethesdensis
, a newly described genus and species within the family
Acetobacteraceae
, was recently isolated from four CGD patients residing in geographically distinct locales who presented with fever and lymphadenitis. We sequenced the genome of the reference strain of
Granulibacter bethesdensis
, which was isolated from lymph nodes of the original patient. The genome contains 2,708,355 base pairs in a single circular chromosome, in which 2,437 putative open reading frames (ORFs) were identified, 1,470 of which share sequence similarity with ORFs in the nonpathogenic but related
Gluconobacter oxydans
genome. Included in the 967 ORFs that are unique to
G. bethesdensis
are ORFs potentially important for virulence, adherence, DNA uptake, and methanol utilization. GC% values and best BLAST analysis suggested that some of these unique ORFs were recently acquired. Comparison of
G. bethesdensis
to other known CGD pathogens demonstrated conservation of some putative virulence factors, suggesting possible common mechanisms involved in pathogenesis in CGD. Genotyping of the four patient isolates by use of a custom microarray demonstrated genome-wide variations in regions encoding DNA uptake systems and transcriptional regulators and in hypothetical ORFs.
G. bethesdensis
is a genetically diverse emerging human pathogen that may have recently acquired virulence factors new to this family of organisms.
Pseudomonas syringae
Lytic Transglycosylases Coregulated with the Type III Secretion System Contribute to the Translocation of Effector Proteins into Plant Cells
Authors: Oh Hye-Sook , Kvitko Brian H. , Morello Joanne E. , Collmer Alan 
Published: September 2007

ABSTRACT

Pseudomonas syringae
translocates virulence effector proteins into plant cells via a type III secretion system (T3SS) encoded by
hrp
(for hypersensitive response and pathogenicity) genes. Three genes coregulated with the Hrp T3SS system in
P. syringae
pv. tomato DC3000 have predicted lytic transglycosylase domains: PSPTO1378 (here designated
hrpH
), PSPTO2678 (
hopP1
), and PSPTO852 (
hopAJ1
).
hrpH
is located between
hrpR
and
avrE1
in the Hrp pathogenicity island and is carried in the functional cluster of
P. syringae
pv. syringae 61
hrp
genes cloned in cosmid pHIR11. Strong expression of DC3000
hrpH
in
Escherichia coli
inhibits bacterial growth unless the predicted catalytic glutamate at position 148 is mutated. Translocation tests involving C-terminal fusions with a Cya (
Bordetella pertussis
adenylate cyclase) reporter indicate that HrpH and HopP1, but not HopAJ1, are T3SS substrates.
Pseudomonas fluorescens
carrying a pHIR11 derivative lacking
hrpH
is poorly able to translocate effector HopA1, and this deficiency can be restored by HopP1 and HopAJ1, but not by HrpH(E148A) or HrpH
1-241
. DC3000 mutants lacking
hrpH
or
hrpH, hopP1
, and
hopAJ1
combined are variously reduced in effector translocation, elicitation of the hypersensitive response, and virulence. However, the mutants are not reduced in secretion of T3SS substrates in culture. When produced in wild-type DC3000, the HrpH(E148A) and HrpH
1-241
variants have a dominant-negative effect on the ability of DC3000 to elicit the hypersensitive response in nonhost tobacco and to grow and cause disease in host tomato. The three Hrp-associated lytic transglycosylases in DC3000 appear to have overlapping functions in contributing to T3SS functions during infection.
Polyphosphate Kinase 1 Is a Pathogenesis Determinant in
Campylobacter jejuni
Authors: Candon Heather L. , Allan Brenda J. , Fraley Cresson D. , Gaynor Erin C. 
Published: September 2007

ABSTRACT

Campylobacter jejuni
is the leading cause of bacterial gastroenteritis in the developed world. Despite its prevalence, relatively little is known about
C. jejuni
's precise pathogenesis mechanisms, particularly in comparison to other well-studied enteric organisms such as
Escherichia coli
and
Salmonella
spp. Altered expression of phosphate genes in a
C. jejuni
stringent response mutant, together with known correlations between the stringent response, polyphosphate (poly-P), and virulence in other bacteria, led us to investigate the role of poly-P in
C. jejuni
stress survival and pathogenesis. All sequenced
C. jejuni
strains harbor a conserved putative polyphosphate kinase 1 predicted to be principally responsible for poly-P synthesis. We generated a targeted
ppk1
deletion mutant (Δ
ppk1
) in
C. jejuni
strain 81-176 and found that Δ
ppk1
, as well as the Δ
spoT
stringent response mutant, exhibited low levels of poly-P at all growth stages. In contrast, wild-type
C. jejuni
poly-P levels increased significantly as the bacteria transitioned from log to stationary phase. Phenotypic analyses revealed that the Δ
ppk1
mutant was defective for survival during osmotic shock and low-nutrient stress. However, certain phenotypes associated with
ppk1
deletion in other bacteria (i.e., motility and oxidative stress) were unaffected in the
C. jejuni
Δ
ppk1
mutant, which also displayed an unexpected increase in biofilm formation. The
C. jejuni
Δ
ppk1
mutant was also defective for the virulence-associated phenotype of intraepithelial cell survival in a tissue culture infection model and exhibited a striking, dose-dependent chick colonization defect. These results indicate that poly-P utilization and accumulation contribute significantly to
C. jejuni
pathogenesis and affect its ability to adapt to specific stresses and stringencies. Furthermore, our study demonstrates that poly-P likely plays both similar and unique roles in
C. jejuni
compared to its roles in other bacteria and that poly-P metabolism is linked to stringent response mechanisms in
C. jejuni
.
The Plant Pathogen
Pantoea ananatis
Produces
N
-Acylhomoserine Lactone and Causes Center Rot Disease of Onion by Quorum Sensing
Authors: Morohoshi Tomohiro , Nakamura Yuta , Yamazaki Go , Ishida Akio , Kato Norihiro , Ikeda Tsukasa 
Published: September 2007

ABSTRACT

A number of gram-negative bacteria have a quorum-sensing system and produce
N
-acyl-
l
-homoserine lactone (AHL) that they use them as a quorum-sensing signal molecule.
Pantoea ananatis
is reported as a common colonist of wheat heads at ripening and causes center rot of onion. In this study, we demonstrated that
P. ananatis
SK-1 produced two AHLs,
N
-hexanoyl-
l
-homoserine lactone (C6-HSL) and
N
-(3-oxohexanoyl)-
l
-homoserine lactone (3-oxo-C6-HSL). We cloned the AHL-synthase gene (
eanI
) and AHL-receptor gene (
eanR
) and revealed that the deduced amino acid sequence of EanI/EanR showed high identity to those of EsaI/EsaR from
P. stewartii
. EanR repressed the
ean
box sequence and the addition of AHLs resulted in derepression of
ean
box. Inactivation of the chromosomal
eanI
gene in SK-1 caused disruption of exopolysaccharide (EPS) biosynthesis, biofilm formation, and infection of onion leaves, which were recovered by adding exogenous 3-oxo-C6-HSL. These results demonstrated that the quorum-sensing system involved the biosynthesis of EPS, biofilm formation, and infection of onion leaves in
P. ananatis
SK-1.
Interplay between the Temperate Phages PY54 and N15, Linear Plasmid Prophages with Covalently Closed Ends
Authors: Hammerl Jens A. , Klein Iris , Appel Bernd , Hertwig Stefan 
Published: September 2007

ABSTRACT

The objective of this study was to determine whether the temperate
Yersinia enterocolitica
phage PY54 may interact with the related
Escherichia coli
phage N15 during both the lysogenic and the lytic cycle in the same cell. The PY54 and N15 prophages are linear plasmids which have been shown to be compatible and stably replicating in
E. coli
and
Yersinia
. In
E. coli
, the PY54 prophage does not restrict N15 propagation. In contrast, N15 reduces by use of its
cor
gene the susceptibility of
Yersinia
strains to PY54. Doubly lysogenic
E. coli
strains release PY54 virions, some of which apparently contain the N15 genome. Further experiments with replicative miniplasmid derivatives of PY54, N15, and the related
Klebsiella oxytoca
phage φKO2 demonstrated that the φKO2 and N15 plasmid prophages belong to the same incompatibility group.
The CbiB Protein of
Salmonella enterica
Is an Integral Membrane Protein Involved in the Last Step of the De Novo Corrin Ring Biosynthetic Pathway
Authors: Zayas Carmen L. , Claas Kathy , Escalante-Semerena Jorge C. 
Published: September 2007

ABSTRACT

We report results of studies of the conversion of adenosylcobyric acid (AdoCby) to adenosylcobinamide-phosphate, the last step of the de novo corrin ring biosynthetic branch of the adenosylcobalamin (coenzyme B
12
) pathway of
Salmonella enterica
serovar Typhimurium LT2. Previous reports have implicated the CbiB protein in this step of the pathway. Hydropathy analysis predicted that CbiB would be an integral membrane protein. We used a computer-generated topology model of the primary sequence of CbiB to guide the construction of CbiB-LacZ and CbiB-PhoA protein fusions, which were used to explore the general topology of CbiB in the cell membrane. A refined model of CbiB as an integral membrane protein is presented. In vivo analyses of the effect of single-amino-acid changes showed that periplasm- and cytosol-exposed residues are critical for CbiB function. Results of in vivo studies also show that ethanolamine-phosphate (EA-P) is a substrate of CbiB, but
l
-Thr-P is not, and that CbiB likely activates AdoCby by phosphorylation. The latter observation leads us to suggest that CbiB is a synthetase not a synthase enzyme. Results from mass spectrometry and bioassay experiments indicate that serovar Typhimurium synthesizes norcobalamin (cobalamin lacking the methyl group at C176) when EA-P is the substrate of CbiB.
The Alanine Racemase of
Mycobacterium smegmatis
Is Essential for Growth in the Absence of
d
-Alanine
Authors: Milligan Daniel L. , Tran Sieu L. , Strych Ulrich , Cook Gregory M. , Krause Kurt L. 
Published: September 2007

ABSTRACT

Alanine racemase, encoded by the gene
alr
, is an important enzyme in the synthesis of
d
-alanine for peptidoglycan biosynthesis. Strains of
Mycobacterium smegmatis
with a deletion mutation of the
alr
gene were found to require
d
-alanine for growth in both rich and minimal media. This indicates that alanine racemase is the only source of
d
-alanine for cell wall biosynthesis in
M. smegmatis
and confirms alanine racemase as a viable target gene for antimycobacterial drug development.
trans
-Acting Factors and
cis
Elements Involved in Glucose Repression of Arabinan Degradation in
Bacillus subtilis
Authors: Inácio José Manuel , de Sá-Nogueira Isabel 
Published: September 2007

ABSTRACT

In
Bacillus subtilis
, the synthesis of enzymes involved in the degradation of arabinose-containing polysaccharides is subject to carbon catabolite repression (CCR). Here we show that CcpA is the major regulator of repression of the arabinases genes in the presence of glucose. CcpA acts via binding to one
cre
each in the promoter regions of the
abnA
and
xsa
genes and to two
cre
s in the
araABDLMNPQ-abfA
operon. The contributions of the coeffectors HPr and Crh to CCR differ according to growth phase. HPr dependency occurs during both exponential growth and the transitional phase, while Crh dependency is detected mainly at the transitional phase. Our results suggest that Crh synthesis may increase at the end of exponential growth and consequently contribute to this effect, together with other factors.
Protein subcellular localization prediction based on compartment-specific features and structure conservation
Authors: Su Emily Chia-Yu , Chiu Hua-Sheng , Lo Allan , Hwang Jenn-Kang , Sung Ting-Yi , Hsu Wen-Lian 
Published: September 2007

Abstract

Background
Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins.

Results
We propose a hybrid prediction method for Gram-negative bacteria that combines a one-versus-one support vector machines (SVM) model and a structural homology approach. The SVM model comprises a number of binary classifiers, in which biological features derived from Gram-negative bacteria translocation pathways are incorporated. In the structural homology approach, we employ secondary structure alignment for structural similarity comparison and assign the known localization of the top-ranked protein as the predicted localization of a query protein. The hybrid method achieves overall accuracy of 93.7% and 93.2% using ten-fold cross-validation on the benchmark data sets. In the assessment of the evaluation data sets, our method also attains accurate prediction accuracy of 84.0%, especially when testing on sequences with a low level of homology to the training data. A three-way data split procedure is also incorporated to prevent overestimation of the predictive performance. In addition, we show that the prediction accuracy should be approximately 85% for non-redundant data sets of sequence identity less than 30%.

Conclusion
Our results demonstrate that biological features derived from Gram-negative bacteria translocation pathways yield a significant improvement. The biological features are interpretable and can be applied in advanced analyses and experimental designs. Moreover, the overall accuracy of combining the structural homology approach is further improved, which suggests that structural conservation could be a useful indicator for inferring localization in addition to sequence homology. The proposed method can be used in large-scale analyses of proteomes.
Oral peptide delivery: in-vitro evaluation of thiolated alginate/poly(acrylic acid) microparticles
Authors: Greimel Alexander , Werle Martin , Bernkop-Schnürch Andreas 
Published: September 2007

Abstract
The purpose of this study was to develop an oral thiomer-based microparticulate delivery system for insulin by ionic gelation. The microparticulate matrix consisted of either poly(acrylic acid)-cysteine (PAA-Cys) and alginate-cysteine (Alg-Cys) or the corresponding unmodified polymers (PAA, Alg). Two different viscosities of alginates were provided for the study, low and medium. Three different types of microparticles were prepared via ionic gelation with calcium (Alg, AlgPAA and AlgPAA-Cys) and their different properties evaluated in-vitro (particle size and shape, drug loading and release profile, swelling and stability). The mean particle size of all formulations ranged from 400 to 600 μm, revealing the lowest for thiolated microparticles. SEM micrographs showed different morphological profiles for the three different types of microparticles. Encapsulation efficiency of insulin increased within the following rank order: Alg (15%) &lt; AlgPAA (40%) &lt; AlgPAA-Cys (65%). Alginate and AlgPAA microparticles displayed a burst release after 30 min, whereas the thiolated particles achieved a controlled release of insulin over 3 h. The swelling ratio was pH dependent: in simulated intestinal fluid microparticles exhibited a much higher water uptake compared with simulated gastric fluid. Due to the formation of intraparticulate disulfide bonds during the preparation process, thiolated particles revealed a higher stability. It was also observed that the viscosity of the two alginates used had no influence on the properties of the particles. According to these results AlgPAA-Cys microparticles obtained by ionic gelation and stabilized via disulfide bonds might be an alternative tool for the oral administration of therapeutic peptides.
Dermal delivery of selected hydrophilic drugs from elastic liposomes: effect of phospholipid formulation and surfactants
Authors: Ita Kevin B , Du Preez Jan , du Plessis Jeanetta , Lane Majella E , Hadgraft Jonathan 
Published: September 2007

Abstract
The effect of phospholipid formulation and choice of surfactant on skin permeation of selected hydrophilic drugs from elastic liposomes across human epidermal membrane has been studied. Sodium cholate and various concentrations of phosphatidylcholine were used for the preparation of liposomes namely hydrogenated phosphatidylcholine 90% (Phospholipon 90H), phosphatidylcholine 95% (Phospholipon 90G), phosphatidylcholine 78.6% (Phospholipon 80), and phosphatidylcholine 50% (Phosal PG). To investigate the effect of the surfactant, liposomes were prepared from 95% phosphatidylcholine (Phospholipon 90G) and various surfactants (sodium cholate, sodium deoxycholate, Span 20 (sorbitan monolaurate), Span 40 (sorbitan monopalmitate), Span 60 (sorbitan stearate) and Span 80 (sorbitan monooleate)). The vesicles were prepared by the conventional rotary evaporation technique. The film was hydrated with phosphate-buffered saline (10 mL) containing 9, 2 and 2.5 mg mL−1 of methotrexate, idoxuridine and aciclovir, respectively. All formulations contained 7% ethanol. Homogenously-sized liposomes were produced following extrusion through 100-nm polycarbonate filters using Lipex Extruder. Particle size was characterized by transmission electron microscopy. Vertical Franz diffusion cells were used for the study of drug delivery through human epidermal membrane. For the three drugs, the highest transcutaneous fluxes were from elastic liposomes containing 95% phosphatidylcholine. In general, a higher flux value was obtained for liposomes containing sodium cholate compared with sodium deoxycholate. For the liposomes containing sorbitan monoesters, there was no clearly defined trend between alkyl chain length and flux values. Overall, transcutaneous fluxes of liposomal preparations of hydrophilic drugs were comparable with those from saturated aqueous solutions (P &gt; 0.05).
Anti-angiogenic, anti-inflammatory and anti-nociceptive activity of 4-hydroxybenzyl alcohol
Authors: Lim Eun-Ju , Jung Hyun-Joo , Park Eun-Hee , Kang Hyun-Jung 
Published: September 2007

Abstract
4-Hydroxybenzyl alcohol (HBA), one of the well-known phenolic compounds in diverse plants, displayed a significant inhibition in the chick chorioallantoic membrane (CAM) angiogenesis assay. HBA was shown to contain an anti-inflammatory activity in carrageenan-induced air pouch model in rats and acetic acid-induced permeability model in mice. Anti-nociceptive activity of HBA was also assessed using the acetic acid-induced writhing test in mice. HBA was able to suppress production of nitric oxide (NO) and expression of inducible nitric oxide synthase (iNOS) in lipopolysaccharide (LPS)-activated RAW264.7 macrophages. In the macrophages, the level of reactive oxygen species (ROS) was diminished by HBA. Taken together, HBA possesses anti-angiogenic, anti-inflammatory and anti-nociceptive activity possibly via its down-regulating activity on NO production, which may be partly responsible for the pharmacological efficacy of several folkloric medicines.