bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Studies of [FeFe] Hydrogenase Maturation in an
Escherichia coli
Biosynthetic System
Authors: King Paul W. , Posewitz Matthew C. , Ghirardi Maria L. , Seibert Michael 
Published: March 2006

ABSTRACT

Maturation of [FeFe] hydrogenases requires the biosynthesis and insertion of the catalytic iron-sulfur cluster, the H cluster. Two radical
S
-adenosylmethionine (SAM) proteins proposed to function in H cluster biosynthesis, HydEF and HydG, were recently identified in the
hydEF-1
mutant of the green alga
Chlamydomonas reinhardtii
(M. C. Posewitz, P. W. King, S. L. Smolinski, L. Zhang, M. Seibert, and M. L. Ghirardi, J. Biol. Chem. 279:25711-25720, 2004). Previous efforts to study [FeFe] hydrogenase maturation in
Escherichia coli
by coexpression of
C. reinhardtii
HydEF and HydG and the HydA1 [FeFe] hydrogenase were hindered by instability of the
hydEF
and
hydG
expression clones. A more stable [FeFe] hydrogenase expression system has been achieved in
E. coli
by cloning and coexpression of
hydE
,
hydF
, and
hydG
from the bacterium
Clostridium acetobutylicum
. Coexpression of the
C. acetobutylicum
maturation proteins with various algal and bacterial [FeFe] hydrogenases in
E. coli
resulted in purified enzymes with specific activities that were similar to those of the enzymes purified from native sources. In the case of structurally complex [FeFe] hydrogenases, maturation of the catalytic sites could occur in the absence of an accessory iron-sulfur cluster domain. Initial investigations of the structure and function of the maturation proteins HydE, HydF, and HydG showed that the highly conserved radical-SAM domains of both HydE and HydG and the GTPase domain of HydF were essential for achieving biosynthesis of active [FeFe] hydrogenases. Together, these results demonstrate that the catalytic domain and a functionally complete set of Hyd maturation proteins are fundamental to achieving biosynthesis of catalytic [FeFe] hydrogenases.
Global Control of Cysteine Metabolism by CymR inBacillus subtilis
Authors: Even Sergine , Burguière Pierre , Auger Sandrine , Soutourina Olga , Danchin Antoine , Martin-Verstraete Isabelle 
Published: March 2006

ABSTRACTYrzC has previously been identified as a repressor controllingytmIexpression via its regulation of YtlI activator synthesis inBacillus subtilis.We identified YrzC as a master regulator of sulfur metabolism. Gene expression profiles ofB. subtilisΔyrzCmutant and wild-type strains grown in minimal medium with sulfate as the sole sulfur source were compared. In the mutant, increased expression was observed for 24 genes previously identified as repressed in the presence of sulfate. Since several genes involved in the pathways leading to cysteine formation were found, we propose to rename YrzC CymR, for “cysteine metabolism repressor.” A CymR-dependent binding to the promoter region of theytlI,ssuB,tcyP,yrrT,yxeK,cysK, orydbMgene was demonstrated using gel shift experiments. A potential CymR target site, TAAWNCN2ANTWNAN3ATMGGAATTW, was found in the promoter region of these genes. In a DNase footprint experiment, the protected region in theytlIpromoter region contained this consensus sequence. Partial deletion or introduction of point mutations in this sequence confirmed its involvement inytlI,yrrT, andyxeKregulation. The addition ofO-acetylserine in gel shift experiments prevented CymR-dependent binding to DNA for all of the targets characterized. Transcriptome analysis of a ΔcymRmutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis.
The Mechanism of the Tyrosine Transporter TyrP Supports a Proton Motive Tyrosine Decarboxylation Pathway in
Lactobacillus brevis
Authors: Wolken Wout A. M. , Lucas Patrick M. , Lonvaud-Funel Aline , Lolkema Juke S. 
Published: March 2006

ABSTRACT

The tyrosine decarboxylase operon of
Lactobacillus brevis
IOEB9809 contains, adjacent to the tyrosine decarboxylase gene, a gene for TyrP, a putative tyrosine transporter. The two genes potentially form a proton motive tyrosine decarboxylation pathway. The putative tyrosine transporter gene of
L. brevis
was expressed in
Lactococcus lactis
and functionally characterized using right-side-out membranes. The transporter very efficiently catalyzes homologous tyrosine-tyrosine exchange and heterologous exchange between tyrosine and its decarboxylation product tyramine. Tyrosine-tyramine exchange was shown to be electrogenic. In addition to the exchange mode, the transporter catalyzes tyrosine uniport but at a much lower rate. Analysis of the substrate specificity of the transporter by use of a set of 19 different tyrosine substrate analogues showed that the main interactions between the protein and the substrates involve the amino group and the phenyl ring with the
para
hydroxyl group. The carboxylate group that is removed in the decarboxylation reaction does not seem to contribute to the affinity of the protein for the substrates significantly. The properties of the TyrP protein are those typical for precursor-product exchangers that operate in proton motive decarboxylation pathways. It is proposed that tyrosine decarboxylation in
L. brevis
results in proton motive force generation by an indirect proton pumping mechanism.
The Integrase of the Conjugative Transposon Tn916Directs Strand- and Sequence-Specific Cleavage of the Origin of Conjugal Transfer,oriT, by the Endonuclease Orf20
Authors: Rocco Jennifer M. , Churchward Gordon 
Published: March 2006

ABSTRACTOrf20 of the conjugative transposon Tn916was purified as a chimeric protein fused to maltose binding protein (MBP-Orf20). The chimeric protein possessed endonucleolytic activity, cleaving both strands of the Tn916origin of conjugal transfer (oriT) at several distinct sites and favoring GT dinucleotides. Incubation of theoriTDNA with purified Tn916integrase (Int) and MBP-Orf20 resulted in strand- and sequence-specific cleavage oforiTat a TGGT motif in the transferred strand. This motif lies immediately adjacent to a sequence inoriTpreviously shown to be protected from DNase I cleavage by Int. The endonucleolytic cleavages produced by Orf20 generated a 3′ OH group that could be radiolabeled by dideoxy ATP and terminal transferase. The production of a 3′ OH group distinguished these Orf20-dependent cleavage events from those catalyzed by Int at the ends of Tn916. Thus, Orf20 functions as the relaxase of Tn916, nickingoriTas the first step in conjugal DNA transfer. Remarkably for a tyrosine recombinase, Tn916Int acts as a specificity factor in the reaction, conferring both strand and sequence specificities on the endonucleolytic cleavage activity of Orf20.
Cyclo(Phe-Pro) Modulates the Expression ofompUinVibriospp
Authors: Park Dae-Kyun , Lee Ko-Eun , Baek Chang-Ho , Kim In Hwang , Kwon Ji-Hyoun , Lee Won Koo , Lee Kyu-Ho , Kim Byung-Soo , Choi Sang-Ho , Kim Kun-Soo 
Published: March 2006

ABSTRACTVibrio vulnificuswas found to produce a chemical that induced the expression ofVibrio fischeri luxgenes. Electron spray ionization-mass spectrometry and1H nuclear magnetic resonance analyses indicated that the compound was cyclo(l-Phe-l-Pro) (cFP). The compound was produced at a maximal level when cell cultures reached the onset of stationary phase. Sodium dodecyl sulfate-polyacrylamide gel analysis of the total proteins ofV. vulnificusindicated that expression of OmpU was enhanced by exogenously added synthetic or purified cFP. AtoxR-null mutant failed to expressompUdespite the addition of cFP. The relatedVibriospp.V. cholerae,V. parahaemolyticus, andV. harveyialso produced cFP, which induced the expression of their ownompUgenes. cFP also enhanced the expression inV. choleraeof thectxgenes, which are known to be regulated by ToxR. Our results suggest that cFP is a signal molecule controlling the expression of genes important for the pathogenicity ofVibriospp.
Identification of New Flagellar Genes ofSalmonella entericaSerovar Typhimurium
Authors: Frye Jonathan , Karlinsey Joyce E. , Felise Heather R. , Marzolf Bruz , Dowidar Naeem , McClelland Michael , Hughes Kelly T. 
Published: March 2006

ABSTRACTRNA levels of flagellar genes in eight different genetic backgrounds were compared to that of the wild type by DNA microarray analysis. Cluster analysis identified new, potential flagellar genes, three putative methyl-accepting chemotaxis proteins, STM3138 (McpA), STM3152 (McpB), and STM3216(McpC), and a CheV homolog, STM2314, inSalmonella, that are not found inEscherichia coli. Isolation and characterization of Mud-lacinsertions incheV,mcpB,mcpC, and the previously uncharacterizedaerlocus ofS. entericaserovar Typhimurium revealed them to be controlled by σ28-dependent flagellar class 3 promoters. In addition, thesrfABCoperon previously isolated as an SsrB-regulated operon clustered with the flagellar class 2 operon and was determined to be under FlhDC control. The previously unclassifiedfliBgene, encoding flagellin methylase, clustered as a class 2 gene, which was verified using reporter fusions, and thefliBtranscriptional start site was identified by primer extension analysis. RNA levels of all flagellar genes were elevated inflgMorfliTnull strains. RNA levels of class 3 flagellar genes were elevated in afliSnull strain, while deletion of thefliY,fliZ, orflkgene did not affect flagellar RNA levels relative to those of the wild type. ThecafA(RNase G) andyhjHgenes clustered with flagellar class 3 transcribed genes. Null alleles incheV,mcpA,mcpB,mcpC, andsrfBdid not affect motility, while deletion ofyhjHdid result in reduced motility compared to that of the wild type.
Coordination between Chromosome Replication, Segregation, and Cell Division inCaulobacter crescentus
Authors: Jensen Rasmus B. 
Published: March 2006

ABSTRACTProgression through theCaulobacter crescentuscell cycle is coupled to a cellular differentiation program. The swarmer cell is replicationally quiescent, and DNA replication initiates at the swarmer-to-stalked cell transition. There is a very short delay between initiation of DNA replication and movement of one of the newly replicated origins to the opposite pole of the cell, indicating the absence of cohesion between the newly replicated origin-proximal parts of theCaulobacterchromosome. The terminus region of the chromosome becomes located at the invaginating septum in predivisional cells, and the completely replicated terminus regions stay associated with each other after chromosome replication is completed, disassociating very late in the cell cycle shortly before the final cell division event. Invagination of the cytoplasmic membrane occurs earlier than separation of the replicated terminus regions and formation of separate nucleoids, which results in trapping of a chromosome on either side of the cell division septum, indicating that there is not a nucleoid exclusion phenotype.
Complete Genome Sequence of the Dehalorespiring Bacterium
Desulfitobacterium hafniense
Y51 and Comparison with
Dehalococcoides ethenogenes
195
Authors: Nonaka Hiroshi , Keresztes Gabor , Shinoda Yoshifumi , Ikenaga Yuko , Abe Miyuki , Naito Kae , Inatomi Kenichi , Furukawa Kensuke , Inui Masayuki , Yukawa Hideaki 
Published: March 2006

ABSTRACT

Desulfitobacterium
strains have the ability to dechlorinate halogenated compounds under
anaerobic conditions by dehalorespiration. The complete genome of the
tetrachloroethene (PCE)-dechlorinating strain
Desulfitobacterium hafniense
Y51 is a 5,727,534-bp
circular chromosome harboring 5,060 predicted protein coding sequences.
This genome contains only two reductive dehalogenase genes, a lower
number than reported in most other dehalorespiring strains. More than
50 members of the dimethyl sulfoxide reductase superfamily and 30
paralogs of the flavoprotein subunit of the fumarate reductase are
encoded as well. A remarkable feature of the genome is the large number
of
O
-demethylase paralogs, which allow utilization of
lignin-derived phenyl methyl ethers as electron donors. The large
genome reveals a more versatile microorganism that can utilize a larger
set of specialized electron donors and acceptors than previously
thought. This is in sharp contrast to the PCE-dechlorinating strain
Dehalococcoides ethenogenes
195, which has a relatively small
genome with a narrow metabolic repertoire. A genomic comparison of
these two very different strains allowed us to narrow down the
potential candidates implicated in the dechlorination process. Our
results provide further impetus to the use of desulfitobacteria as
tools for
bioremediation.
Global Gene Expression Analysis of Iron-Inducible Genes in
Magnetospirillum magneticum
AMB-1
Authors: Suzuki Takeyuki , Okamura Yoshiko , Calugay Ronie J. , Takeyama Haruko , Matsunaga Tadashi 
Published: March 2006

ABSTRACT

Iron uptake systems were identified by global expression profiling of
Magnetospirillum magneticum
AMB-1.
feo
,
tpd
, and
ftr
, which encode ferrous iron transporters, were up-regulated under iron-rich conditions. The concomitant rapid iron uptake and magnetite formation suggest that these uptake systems serve as iron supply lines for magnetosome synthesis.
Harpin Mediates Cell Aggregation in
Erwinia chrysanthemi
3937
Authors: Mee-Ngan Yap , Rojas Clemencia M. , Yang Ching-Hong , Charkowski Amy O. 
Published: March 2006

ABSTRACT

The hypersensitive response elicitor harpin (HrpN) of soft rot pathogen
Erwinia chrysanthemi
strains 3937 and EC16 is secreted via the type III secretion system and remains cell surface bound. Strain 3937 HrpN is essential for cell aggregation, but the C-terminal one-third of the protein is not required for aggregative activity.
Simplified Phenotypic Scheme Evaluated by 16S rRNA Sequencing for Differentiation between
Yersinia enterocolitica
and
Y. enterocolitica
-Like species
Authors: Hallanvuo Saija , Peltola Joanna , Heiskanen Tarja , Siitonen Anja 
Published: March 2006

ABSTRACT

Many clinical laboratories are familiar with a sizeable group of “unserotypeable
Yersinia enterocolitica
” strains. Due to identification problems, this group may hide
Y. bercovieri
,
Y. mollaretii
, and
Y. rohdei
strains. We present a simple scheme to distinguish between pathogenic
Y. enterocolitica
and potentially nonpathogenic
Y. enterocolitica-
like strains.
Molecular Characterization of Wild-Type Polioviruses Isolated in Greece during the 1996 Outbreak in Albania
Authors: Kyriakopoulou Zaharoula , Kottaridi Christine , Dedepsidis Evaggelos , Bolanaki Eugenia , Levidiotou-Stefanou Stamatina , Markoulatos Panayotis 
Published: March 2006

ABSTRACT
During the present study three type 1 poliovirus strains isolated in Greece during the 1996 poliomyelitis outbreak in Albania were retrospectively investigated and determination of their relationship with other epidemic strains isolated in Albania or elsewhere during previous epidemics was attempted. SimPlot analysis revealed that the three Greek strains are the result of a recombination event in the VP2 coding region.
Ulocladium atrum
Keratitis
Authors: Badenoch P. R. , Halliday C. L. , Ellis D. H. , Billing K. J. , Mills R. A. D. 
Published: March 2006

ABSTRACT

We report a case of
Ulocladium atrum
keratitis in a 43-year-old man. No predisposing event was known. He received natamycin and fluconazole drops and the infection resolved. The isolate was identified by morphological and rRNA gene sequence analyses.
U. atrum
is a dematiaceous hyphomycete not hitherto reported to infect humans.
Rapid Screening of Fluoroquinolone Resistance Determinants in
Streptococcus pneumoniae
by PCR-Restriction Fragment Length Polymorphism and Single-Strand Conformational Polymorphism
Authors: Ip Margaret , Chau Shirley S. L. , Chi Fang , Qi Amy , Lai Raymond W. M. 
Published: March 2006

ABSTRACT

A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in
Streptococcus pneumoniae
. One hundred nonduplicate
Streptococcus pneumoniae
isolates with ciprofloxacin MICs of ≥4.0 μg/ml from the Prince of Wales Hospital, Hong Kong, years 2000 to 2003, were examined. For each isolate, PCR amplicons of quinolone resistance-determining regions (QRDRs) of
gyrA
,
gyrB
,
parC
, and
parE
genes were digested with AluI, HinfI, Sau3AI, and MspI, respectively, and analyzed by SSCP. Each SSCP pattern was given a number, and each isolate obtained a four-digit code, e.g., 1111, that represented the SSCP profile. The SSCP patterns were correlated to mutations characterized from sequence analyses of PCR amplicons. The most common SSCP profile obtained was no. 5232 (40%), which included strains with two amino acid substitutions in the ParC (Lys-137-Asn) and ParE (Ile-460-Val) genes, followed by the SSCP profile 5223 (17%), which included strains with amino acid substitutions in the ParE (Ile-460-Val) gene only. Ten isolates (10%) with amino acid substitutions at GyrA and ParE (±ParC) genes were resistant to levofloxacin with a MIC of ≥16 μg/ml. Other SSCP profiles were unique in distinguishing the common amino acid substitutions in GyrA (Ser-81-Phe) and ParC (Lys-137-Asn, Ser-79-Phe plus Lys-137-Asn, Asp-83-Asn plus Lys-137-Asn, Ser-79-Phe, and Glu-96-Asp). SSCP analysis of restricted fragments generated patterns that were highly discriminative for mutations present in the QRDRs of
gyrA
,
gyrB
,
parC
, and
parE
. This method provides a database of high resolution profiles on these mutations and allows rapid screening for new mutations of the fluoroquinolone resistance genes.
Pre- and Postvaccination Clonal Compositions of Invasive Pneumococcal Serotypes for Isolates Collected in the United States in 1999, 2001, and 2002
Authors: Beall Bernard , McEllistrem M. Catherine , Gertz Robert E. , Wedel Stephanie , Boxrud David J. , Gonzalez Antonio L. , Medina Marie-Jo , Pai Rekha , Thompson Terry A. , Harrison Lee H. , McGee Lesley , Whitney Cynthia G. ,   the Active Bacterial Core Surveillance Team
Published: March 2006

ABSTRACTMonitoring of serotypes and their clonal associations is critical as pneumococci adapt to the selective pressures exerted by the pneumococcal seven-valent conjugate vaccine (PCV7). We genotyped 1,476 invasive isolates from the Active Bacterial Core surveillance (705 [89.8%] of the isolates were obtained from children <5 years of age, and 771 [18.4%] of the isolates were obtained from individuals >5 years of age) in 2001 and 2002 (after the introduction of PCV7). The data were compared to the results for 1,168 invasive isolates (855 [83.9%] of the isolates were from children <5 years of age) collected in 1999. Among children <5 years of age, the incidence of invasive disease due to non-PCV7 serogroups together with serogroup 19A increased (P< 0.001). Eighty-three clonal sets, representing 177 multilocus sequence types (STs), were compiled from the 3-year isolate set. Among the non-PCV7 serogroups, newly emerging clones were uncommon; and a significant expansion of already established clones occurred for serotypes 3 (ST180), 7F (ST191), 15BCF (ST199), 19A (ST199), 22F (ST433), 33F (ST662), and 38 (ST393). However, additional minor clonal types within serotypes 1, 6A, 6B, 7C, 9N, 10A, 12F, 14, 15B/C, 17F, 19A, 19F, 20, 22F, and 33F that were absent in 1999 were found during 2001 and 2002. Although 23 clonal sets exhibited multiple serotypes, for most serotypes there were either no changes or modest changes in clonal compositions since the introduction of PCV7. The only example of an identical ST shared between non-PCV7 and PCV7 or PCV7-related serotypes was ST199; however, ST199 was prevalent within serotypes 15B/C and 19A before and after PCV7 introduction. Continued genotypic surveillance is warranted, since certain clones not targeted by PCV7 are expanding, and their emergence as significant pathogens could occur with maintained vaccine pressure.
Ethnic differences in control of cardiovascular risk factors in patients with type 2 diabetes attending an Inner London diabetes clinic
Authors: Chowdhury T A , Lasker S S , Mahfuz R 
Published: March 2006

Abstract

Background
South Asians have higher risk of diabetic complications compared with white Europeans. The aim of this study was to compare management of cardiovascular risk factors between Bangladeshis and white Europeans.

Methods
A retrospective survey of all diabetic patients attending an Inner London hospital diabetic clinic over one year was undertaken. Data were obtained from the hospital diabetes database: presence of macrovascular (myocardial infarction, angina, stroke, transient ischaemic attack, cardiac intervention) and microvascular disease (neuropathy, retinopathy, and nephropathy), glycated haemoglobin, blood pressure, lipids, smoking, and body mass index (BMI) were all determined.

Results
A total of 1162 white European and 912 Bangladeshi patients with full data available were included in the analyses. The groups were equivalent in age, sex, duration of diabetes. Compared with white Europeans, Bangladeshis had more macrovascular disease (19.5% v 11.9% p&lt;0.01), sight threatening retinopathy (7.2% v 3.8%, p&lt;0.01), and nephropathy (15.3% v 9.1%, p&lt;0.01). In addition, Bangladeshis had significantly more male smokers (28.1% v 22.1%, p&lt;0.01), poorer glycaemic control (mean HbA1c 8.6% v 8.1%, p = 0.039), greater proportion with uncontrolled hypercholesterolaemia (total cholesterol &gt;5.0 mmol/l, 31.6% v 26% p = 0.05), and poorer control of blood pressure (proportion with BP &gt;140/80 mm Hg, 43.2% v 32.1%, p&lt;0.01).

Conclusions
South Asians with type 2 diabetes have poorer glycaemic, blood pressure, and lipid control than white Europeans. The reasons for this are probably multifactorial.
Ventilator associated pneumonia
Authors: Hunter J D 
Published: March 2006

Abstract
Hospital acquired or nosocomial infections continue to be an important cause of morbidity and mortality. The critically ill patient is at particular risk of developing intensive care unit acquired infection, with the lungs being especially vulnerable. Nosocomial bacterial pneumonia occurring after two days of mechanical ventilation is referred to as ventilator associated pneumonia, and is the most common nosocomial infection seen in the intensive care unit. Intubation of the trachea and mechanical ventilation is associated with a 7-fold to 21-fold increase in the incidence of pneumonia and up to 28% of patients receiving mechanical ventilation will develop this complication. Its development is associated with an attributable increase in morbidity and mortality. The establishment of an accurate diagnosis of ventilator associated pneumonia remains problematic and as yet there is still no accepted “gold standard” for diagnosis. The responsible pathogens vary according to case mix, local resistance patterns, and methodology of sampling. However, there is general agreement that rapid initiation of appropriate antimicrobial therapy improves outcome.