bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Regulation of the
Staphylococcus aureus
Thioredoxin and Thioredoxin Reductase Genes in Response to Oxygen and Disulfide Stress
Authors: Uziel Orit , Borovok Ilya , Schreiber Rachel , Cohen Gerald , Aharonowitz Yair 
Published: December 2003

ABSTRACT

In this report we describe the cloning, organization, and promoter analysis of the
Staphylococcus aureus
thioredoxin (
trxA
) and thioredoxin reductase (
trxB
) genes and their transcription in response to changes in oxygen concentration and to oxidative stress compounds. Northern analysis showed that the
S. aureus trxA
and
trxB
genes were transcribed equally well in aerobic and anaerobic conditions. Several oxidative stress compounds were found to rapidly induce transcription of the
trxA
and
trxB
genes. The most pronounced effects were seen with diamide, a thiol-specific oxidant that promotes disulfide bond formation; menadione, a redox cycling agent; and τ-butyl hydroperoxide, an organic peroxide. In each case the induction was independent of the general stress sigma factor σ
B
. These studies show that the
S. aureus trxA
and
trxB
genes are upregulated following exposure to these oxidative stress agents, resulting in increased disulfide bond formation. In contrast, no effect of hydrogen peroxide on induction of the
trxA
and
trxB
genes was seen. We also show that the
S. aureus
thioredoxin reductase appears to be essential for growth. This observation, coupled with structural differences between the bacterial and mammalian thioredoxin reductases, suggests that it may serve as a target for the development of new antimicrobials.
Identification of the LIV-I/LS System as the Third Phenylalanine Transporter in
Escherichia coli
K-12
Authors: Koyanagi Takashi , Katayama Takane , Suzuki Hideyuki , Kumagai Hidehiko 
Published: December 2003

ABSTRACT

In
Escherichia coli
, the active transport of phenylalanine is considered to be performed by two different systems, AroP and PheP. However, a low level of accumulation of phenylalanine was observed in an aromatic amino acid transporter-deficient
E. coli
strain (Δ
aroP
Δ
pheP
Δ
mtr
Δ
tna
Δ
tyrP
). The uptake of phenylalanine by this strain was significantly inhibited in the presence of branched-chain amino acids. Genetic analysis and transport studies revealed that the LIV-I/LS system, which is a branched-chain amino acid transporter consisting of two periplasmic binding proteins, the LIV-binding protein (LIV-I system) and LS-binding protein (LS system), and membrane components, LivHMGF, is involved in phenylalanine accumulation in
E. coli
cells. The

K
m

values for phenylalanine in the LIV-I and LS systems were determined to be 19 and 30 μM, respectively. Competitive inhibition of phenylalanine uptake by isoleucine, leucine, and valine was observed for the LIV-I system and, surprisingly, also for the LS system, which has been assumed to be leucine specific on the basis of the results of binding studies with the purified LS-binding protein. We found that the LS system is capable of transporting isoleucine and valine with affinity comparable to that for leucine and that the LIV-I system is able to transport tyrosine with affinity lower than that seen with other substrates. The physiological importance of the LIV-I/LS system for phenylalanine accumulation was revealed in the growth of phenylalanine-auxotrophic
E. coli
strains under various conditions.
Participation of
fad
and
mbt
Genes in Synthesis of Mycobactin in
Mycobacterium smegmatis
Authors: LaMarca B. Babbette D. , Zhu Wenming , Arceneaux Jean E. L. , Byers B. Rowe , Lundrigan Michael D. 
Published: December 2003

ABSTRACT

Colonies of
Mycobacterium smegmatis
LR222 on iron-limiting (0.1 μM Fe) minimal medium agar fluoresce under UV light due to the accumulation in the cells of the deferri form of the siderophore mycobactin. Two mutants with little or no fluorescence, designated LUN8 and LUN9, were isolated by screening colonies of transposon (Tn
611
)-mutagenized
M. smegmatis
. Ferrimycobactin prepared from iron-restricted cells of the wild type had an
R

f

of 0.62 on high-performance thin-layer chromatography (HPTLC) and a characteristic visible absorption spectrum with a peak near 450 nm. Similar extracts from LUN8 cells contained a small amount of ferrimycobactin with an
R

f

of 0.58 on HPTLC and an absorption spectrum with the peak shifted to a wavelength lower than that of the wild-type ferrimycobactin. Nuclear magnetic resonance spectroscopy studies suggested that the LUN8 mycobactin may have an altered fatty acid side chain. Mutant strain LUN9 produced no detectable mycobactin. Neither mutant strain produced measurable amounts of excreted mycobactin, although both excreted exochelin (the mycobacterial peptido-hydroxamate siderophore), and both mutants were more sensitive than the wild-type strain to growth inhibition by the iron chelator ethylenediamine-di(
o
-hydroxyphenylacetic acid). The transposon insertion sites were identified, and sequence analyses of the cloned flanking chromosome regions showed that the mutated gene in LUN9 was an orthologue of the
Mycobacterium tuberculosis
mycobactin biosynthetic gene
mbtE
. The mutated gene in LUN8 had homology with
M. tuberculosis fadD33
(
Rv1345
), a gene that may encode an acyl-coenzyme A synthase and which previously was not known to participate in synthesis of mycobactin.
Structural and Genetic Characterization of the
Shigella boydii
Type 13 O Antigen
Authors: Feng Lu , Senchenkova Sof'ya N. , Yang Jinghua , Shashkov Alexander S. , Tao Jiang , Guo Hongjie , Zhao Guang , Knirel Yuriy A. , Reeves Peter , Wang Lei 
Published: December 2003

ABSTRACT

Shigella
is an important human pathogen. It is generally agreed that
Shigella
and
Escherichia coli
constitute a single species; the only exception is
Shigella boydii
type 13, which is more distantly related to
E. coli
and other
Shigella
forms and seems to represent another species. This gives
S. boydii
type 13 an important status in evolution. O antigen is the polysaccharide part of the lipopolysaccharide in the outer membrane of gram-negative bacteria and plays an important role in pathogenicity. The chemical structure and genetic organization of the
S. boydii
type 13 O antigen were investigated. The O polysaccharide was found to be acid labile owing to the presence of a glycosyl phosphate linkage in the main chain. The structure of the linear pentasaccharide phosphate repeating unit (O unit) was established by nuclear magnetic resonance spectroscopy, including two-dimensional COSY, TOCSY, ROESY, and H-detected
1
H,
13
C and
1
H,
31
P HMQC experiments, along with chemical methods. The O antigen gene cluster of
S. boydii
type 13 was located and sequenced. Genes for synthesis of UDP-2-acetamido-2,6-dideoxy-
l
-glucose and genes that encode putative sugar transferases, O unit flippase, and O antigen polymerase were identified. Seven genes were found to be specific to
S. boydii
type 13. The
S. boydii
type 13 O antigen gene cluster has higher levels of sequence similarity with
Vibrio cholerae
gene clusters and may be evolutionarily related to these gene clusters.
Complete Sequence and Evolutionary Genomic Analysis of the
Pseudomonas aeruginosa
Transposable Bacteriophage D3112
Authors: Wang Pauline W. , Chu Linda , Guttman David S. 
Published: December 2003

ABSTRACT

Bacteriophage D3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen
Pseudomonas aeruginosa
. To further our understanding of transposable phage in
P. aeruginosa
, we have sequenced the complete genome of D3112. The genome is 37,611 bp, with an overall G+C content of 65%. We have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes A and B) that have been previously characterized and sequenced. The organization of the putative coding regions corresponds to published genetic and transcriptional maps and is very similar to that of enterobacteriophage Mu. In contrast, the International Committee on Taxonomy of Viruses has classified D3112 as a λ-like phage on the basis of its morphology. Similarity-based analyses identified 27 open reading frames with significant matches to proteins in the NCBI databases. Forty-eight percent of these were similar to Mu-like phage and prophage sequences, including proteins responsible for transposition, transcriptional regulation, virion morphogenesis, and capsid formation. The tail proteins were highly similar to prophage sequences in
Escherichia coli
and phage Phi12 from
Staphylococcus aureus
, while proteins at the right end were highly similar to proteins in
Xylella fastidiosa
. We performed phylogenetic analyses to understand the evolutionary relationships of D3112 with respect to Mu-like versus λ-like bacteriophages. Different results were obtained from similarity-based versus phylogenetic analyses in some instances. Overall, our findings reveal a highly mosaic structure and suggest that extensive horizontal exchange of genetic material played an important role in the evolution of D3112.
The HWE Histidine Kinases, a New Family of Bacterial Two-Component Sensor Kinases with Potentially Diverse Roles in Environmental Signaling
Authors: Karniol Baruch , Vierstra Richard D. 
Published: December 2003

ABSTRACT

Two-component signal transduction pathways play a major role in the response of bacteria to external cues. These pathways are initiated by large collection of histidine kinases (HKs) containing a sensor domain that perceives the environmental signal followed by an HK domain that triggers a histidine-aspartate phosphorelay. Previous phylogenetic analyses identified 11 major families of two-component HKs by comparing signature motifs within the HK domain. Here we describe a new family with homology to
Agrobacterium tumefaciens
BphP2, an HK first discovered by the presence of a phytochrome sensor domain involved in light perception. Members of this sensor HK family differ from most others by the absence of a recognizable F box and the presence of several uniquely conserved residues, including a histidine in the N box and a tryptophan-X-glutamic acid sequence in the G1 box, which we have used to define the family (HWE). At least 81 members were identified in a variety of α- and γ-proteobacteria, with a significant enrichment in the
Rhizobiaceae
family. Several representatives were shown to have HK activity in vitro, supporting their proposed participation in phosphorelays. One or more domains related to signal transduction were evident N-terminal to the HK domain, including chemotactic methyltransferase domains, suggesting that this family has multiple roles in environmental signaling. The discovery of the HWE family further extends the diversity within the HK superfamily and expands the importance of two-component signaling in bacteria.
TheacnDGenes ofShewenella oneidensisandVibrio choleraeEncode a New Fe/S-Dependent 2-Methylcitrate Dehydratase Enzyme That RequiresprpFFunction In Vivo
Authors: Grimek Tracey L. , Escalante-Semerena Jorge C. 
Published: December 2003

ABSTRACTThe propionate utilization operons of several bacteria differ from each other in the occurrence of two genes,acnDandprpF, in place of or in addition to theprpDgene encoding an Fe/S-independent 2-methylcitrate dehydratase enzyme. We cloned theacnDandprpFgenes from two organisms,Shewanella oneidensisandVibrio cholerae, and found that, together, the AcnD and PrpF proteins restored the ability of aprpDmutant strain ofSalmonella entericato grow on propionate as a source of carbon and energy. However, neitheracnDnorprpFalone was able to substitute forprpD. The AcnD and PrpF proteins were isolated and biochemically analyzed. The AcnD protein required reconstitution of an Fe/S cluster for activity. All detectable AcnD activity was lost after incubation with iron-chelating agents, and no AcnD activity was observed after attempted reconstitution without iron. Nuclear magnetic resonance spectroscopy and in vitro activity assay data showed that AcnD dehydrated 2-methylcitrate and citrate to 2-methyl-cis-aconitate andcis-aconitate, respectively; AcnD also hydratedcis-aconitate. However, 2-methylisocitrate and isocitrate were not substrates for AcnD, indicating that AcnD only catalyzes the first half of the aconitase-like dehydration reactions. No aconitase-like activity was found for PrpF. It is hypothesized that, in vivo, PrpF is an accessory protein required to prevent oxidative damage of the Fe/S center of active AcnD enzyme or that it may be involved in synthesis or repair of the Fe/S cluster present in AcnD.
Genetic Analysis of the Cell Division Protein FtsI (PBP3): Amino Acid Substitutions That Impair Septal Localization of FtsI and Recruitment of FtsN
Authors: Wissel Mark C. , Weiss David S. 
Published: December 2003

ABSTRACT

FtsI (also called PBP3) of
Escherichia coli
is a transpeptidase required for synthesis of peptidoglycan in the division septum and is one of several proteins that localize to the septal ring. FtsI comprises a small cytoplasmic domain, a transmembrane helix, a noncatalytic domain of unknown function, and a catalytic (transpeptidase) domain. The last two domains reside in the periplasm. We used PCR to randomly mutagenize
ftsI
, ligated the products into a green fluorescent protein fusion vector, and screened ∼7,500 transformants for
gfp-ftsI
alleles that failed to complement an
ftsI
null mutant. Western blotting and penicillin-binding assays were then used to weed out proteins that were unstable, failed to insert into the cytoplasmic membrane, or were defective in catalysis. The remaining candidates were tested for septal localization and ability to recruit another division protein, FtsN, to the septal ring. Mutant proteins severely defective in localization to the septal ring all had lesions in one of three amino acids—R23, L39, or Q46—that are in or near the transmembrane helix and implicate this region of FtsI in septal localization. Mutant FtsI proteins defective in recruitment of FtsN all had lesions in one of eight residues in the noncatalytic domain. The most interesting of these mutants had lesions at G57, S61, L62, or R210. Although separated by ∼150 residues in the primary sequence, these amino acids are close together in the folded protein and might constitute a site of FtsI-FtsN interaction.
TREATMENT OF NECK PAIN AFTER WHIPLASH INJURIES WITH BOTULINUM TOXIN-A INJECTIONS
Authors: Juan Francisco J. 
Published: December 2003

Objective: Botulinum toxin has demonstrated efficacy in a variety of conditions associated with muscle spasm. We report our experience with botulinum toxin-A in patients with neck pain after whiplash associated disorders. Methods: A descriptive epidemiology study and case reports of patients treated with botulinum toxin type-A (Botox®) for neck pain after whiplash injuries were performed over a three-year period. A total of 31 patients who had received botulinum toxin-A for neck pain were studied. Patients were treated with 50–75 units of Botox®. Clinical follow-up evaluation was performed with repeated examinations that included range of movement (ROM), visual analogue scale (VAS), and neck pain disability index (NPDI). After initial assessment and treatment patients were followed-up 8 weeks. Results: Of 31 patients, 67.7% had excellent response rates. There was a significant reduction in pain as well as improvement in the ROM. 77.4% of patients responded significantly (p<0.05) to botulinum toxin-A injection with reduction in pain. Conclusion: The use of botulinum toxin type-A in patients with neck pain associated to whiplash injury resulted in significant improvement in subjective pain. This therapy is safe. These results suggest the need for a double-blind trial on the use of botulinum toxin during chronic phase. Also, the treatment of the subacute or acute phase of whiplash associated disorders should be investigated.
A genome-wide scan to identify loci for smoking rate in the Framingham Heart Study population
Authors: Li Ming D , Ma Jennie Z , Cheng Rong , Dupont Randolph T , Williams Nancy J , Crews Karen M , Payne Thomas J , Elston Robert C 
Published: December 2003

Abstract
Background
Although many years of genetic epidemiological studies have demonstrated that genetics plays a significant role in determining smoking behavior, little information is available on genomic loci or genes affecting nicotine dependence. Several susceptibility chromosomal regions for nicotine dependence have been reported, but few have received independent confirmation. To identify susceptibility loci for nicotine dependence, 313 extended pedigrees selected from the Framingham Heart Study population were analyzed by both the GENEHUNTER and S.A.G.E. programs.

Results
After performing linkage analyses on the 313 extended Framingham Heart Study families, the EM Haseman-Elston method implemented in GENEHUNTER provided evidence for significant linkage of smoking rate to chromosome 11 and suggestive linkage to chromosomes 9, 14, and 17. Multipoint sib-pair regression analysis using the SIBPAL program of S.A.G.E. on 1389 sib pairs that were split from the 313 extended families identified suggestive linkage of smoking rate to chromosomes 4, 7, and 17. Of these identified positive regions for nicotine dependence, loci on chromosomes 7, 11, and 17 were identified by both GENEHUNTER and S.A.G.E. programs.

Conclusion
Our genome-wide scan results on the Framingham Heart Study data provide evidence for significant linkage of smoking rate to chromosome 11 and suggestive linkage to chromosomes 4, 7, 9, 14, and 17. These findings suggest that some of these regions may harbor susceptibility loci for nicotine dependence, and warrant further investigation in this and other populations.
Genome-wide linkage analysis of longitudinal phenotypes using σ2
A random effects (SSARs) fitted by Gibbs sampling
Authors: Palmer Lyle J , Scurrah Katrina J , Tobin Martin , Patel Sanjay R , Celedon Juan C , Burton Paul R , Weiss Scott T 
Published: December 2003

AbstractThe study of change in intermediate phenotypes over time is important in genetics. In this paper we explore a new approach to phenotype definition in the genetic analysis of longitudinal phenotypes. We utilized data from the longitudinal Framingham Heart Study Family Cohort to investigate the familial aggregation and evidence for linkage to change in systolic blood pressure (SBP) over time. We used Gibbs sampling to derive sigma-squared-A-random-effects (SSARs) for the longitudinal phenotype, and then used these as a new phenotype in subsequent genome-wide linkage analyses.Additive genetic effects (σ2A.time) were estimated to account for ~9.2% of the variance in the rate of change of SBP with age, while additive genetic effects (σ2A) were estimated to account for ~43.9% of the variance in SBP at the mean age. The linkage results suggested that one or more major loci regulating change in SBP over time may localize to chromosomes 2, 3, 4, 6, 10, 11, 17, and 19. The results also suggested that one or more major loci regulating level of SBP may localize to chromosomes 3, 8, and 14.Our results support a genetic component to both SBP and change in SBP with age, and are consistent with a complex, multifactorial susceptibility to the development of hypertension. The use of SSARs derived from quantitative traits as input to a conventional linkage analysis appears to be valuable in the linkage analysis of genetically complex traits. We have now demonstrated in this paper the use of SSARs in the context of longitudinal family data.
Sibling recurrence risk ratio analysis of the metabolic syndrome and its components over time
Authors: Chen Wei J , Liu Pi-Hua , Ho Yen-Yi , Chien Kuo-Liong , Lo Min-Tzu , Shih Wei-Liang , Yen Yu-Chun , Lee Wen-Chung 
Published: December 2003

Abstract
Background
The purpose of this study was to estimate both cross-sectional sibling recurrence risk ratio (λ
s
) and lifetime λ
s
for the metabolic syndrome and its individual components over time among sibships in the prospectively followed-up cohorts provided by the Genetic Analysis Workshop 13. Five measures included in the operational criteria of the metabolic syndrome by the Adult Treatment Panel III were examined. A method for estimating sibling recurrence risk with correction for complete ascertainment was used to estimate the numerator, and the prevalence in the whole cohort was used as the denominator of λ
s
.

Results
Considerable variability in the λ
s
was found in terms of different time-points for the cross-sectional definition, the times of fulfilling the criterion for lifetime definition, and different components. Obesity and hyperglycemia had the highest cross-sectional λ
s
of the five components. Both components also had the largest slopes in the linear trend of the lifetime λ
s
. However, the magnitudes of the lifetime λ
s
were similar to that of the mean cross-sectional λ
s
, which were <2. The results of nonparametric linkage analysis showed only suggestive evidence of linkage between one marker and lifetime diagnosis of low high-density lipoprotein cholesterol and metabolic syndrome, respectively.

Conclusion
The λ
s
of the metabolic syndrome and its components varies substantially across time, and the λ
s
of lifetime diagnosis was not necessarily larger than that of a cross-sectional diagnosis. The magnitude of λ
s
does not predict well the maximum LOD score of linkage analysis.
Lack of reproducibility of linkage results in serially measured blood pressure data
Authors: Patel Sanjay R , Celedon Juan C , Weiss Scott T , Palmer Lyle J 
Published: December 2003

Abstract
Background
Using the longitudinal Framingham Heart Study data on blood pressure, we analyzed the reproducibility of linkage measures from serial cross-sectional surveys of a defined population by performing genome-wide model-free linkage analyses to systolic blood pressure (SBP) and history of hypertension (HTN) measured at five separate time points.

Results
The heritability of SBP was relatively stable over time, ranging from 11.6 to 23.5% (coefficient of variation = 25.7%). However, the variability in linkage results was much greater. The average correlation in LOD scores at any pair of time points was 0.46 for HTN (NPL All LOD) and 0.17 for SBP (Variance Components LOD). No evidence of reproducible linkage results was found, with a mean κ of 0.02 for linkage to HTN and -0.03 for SBP linkage. At loci with potential evidence for linkage (LOD > 1.0 at one or more time points), the correlation was even lower. The coefficient of variation at loci with potential evidence of linkage was 126% for HTN and 135% for SBP. None of 15 chromosomal regions for HTN and only one of 28 regions for SBP with potential evidence for linkage had a LOD > 1.0 at more than two of the five time points.

Conclusion
These data suggest that, although heritability estimates at different time points are relatively robust, the reproducibility of linkage results in serial cross-sectional samples of a geographically defined population at successive time points is poor. This may explain in part the difficulty encountered in replicating linkage studies of complex phenotypes.