bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corynebacterium diphtheriae
: Identification and Characterization of a Channel-Forming Protein in the Cell Wall
Authors: Schiffler Bettina , Barth Enrico , Daffé Mamadou , Benz Roland 
Published: August 2007

ABSTRACT

The cell wall fraction of the gram-positive, nontoxic
Corynebacterium diphtheriae
strain C8
r
(−) Tox
−
(= ATCC 11913) contained a channel-forming protein, as judged from reconstitution experiments with artificial lipid bilayer experiments. The channel-forming protein was present in detergent-treated cell walls and in extracts of whole cells obtained using organic solvents. The protein had an apparent molecular mass of about 66 kDa as determined on Tricine-containing sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels and consisted of subunits having a molecular mass of about 5 kDa. Single-channel experiments with the purified protein suggested that the protein formed channels with a single-channel conductance of 2.25 nS in 1 M KCl. Further single-channel analysis suggested that the cell wall channel is wide and water filled because it has only slight selectivity for cations over anions and its conductance followed the mobility sequence of cations and anions in the aqueous phase. Antibodies raised against PorA, the subunit of the cell wall channel of
Corynebacterium glutamicum
, detected both monomers and oligomers of the isolated protein, suggesting that there are highly conserved epitopes in the cell wall channels of
C. diphtheriae
and PorA. Localization of the protein on the cell surface was confirmed by an enzyme-linked immunosorbent assay. The prospective homology of PorA with the cell wall channel of
C. diphtheriae
was used to identify the cell wall channel gene,
cdporA
, in the known genome of
C. diphtheriae
. The gene and its flanking regions were cloned and sequenced. CdporA is a protein that is 43 amino acids long and does not have a leader sequence.
cdporA
was expressed in a
C. glutamicum
strain that lacked the major outer membrane channels PorA and PorH. Organic solvent extracts of the transformed cells formed in lipid bilayer membranes the same channels as the purified CdporA protein of
C. diphtheriae
formed, suggesting that the expressed protein is able to complement the PorA and PorH deficiency of the
C. glutamicum
strain. The study is the first report of a cell wall channel in a pathogenic
Corynebacterium
strain.
The Peptidyl-Prolyl Isomerase Activity of SlyD Is Not Required for Maturation of
Escherichia coli
Hydrogenase
Authors: Zhang Jie Wei , Leach Michael R. , Zamble Deborah B. 
Published: August 2007

ABSTRACT

Escherichia coli
SlyD, which is involved in the biosynthesis of the metal cluster in the [NiFe]-hydrogenase enzymes, exhibits several activities including that of a peptidyl-prolyl isomerase (PPIase). Mutations that result in deficient PPIase activity do not produce corresponding decreases in the other activities of SlyD in vitro or in hydrogenase production levels in vivo.
New Locus Important for
Myxococcus
Social Motility and Development
Authors: Zhang Cui-ying , Cai Ke , Liu Hong , Zhang Yong , Pan Hong-wei , Wang Bing , Wu Zhi-hong , Hu Wei , Li Yue-zhong 
Published: August 2007

ABSTRACT

The
mts
locus in salt-tolerant
Myxococcus fulvus
HW-1 was found to be critical for gliding motility, fruiting-body formation, and sporulation. The homologous genes in
Myxococcus xanthus
are also important for social motility and fruiting-body development. The
mts
genes were determined to be involved in cell-cell cohesion in both myxobacterial species.
Activation of
yeaR-yoaG
Operon Transcription by the Nitrate-Responsive Regulator NarL Is Independent of Oxygen- Responsive Regulator Fnr in
Escherichia coli
K-12
Authors: Lin Hsia-Yin , Bledsoe Peggy J. , Stewart Valley 
Published: August 2007

ABSTRACT

The facultative aerobe
Escherichia coli
K-12 can use respiratory nitrate ammonification to generate energy during anaerobic growth. The toxic compound nitric oxide is a by-product of this metabolism. Previous transcript microarray studies identified the
yeaR-yoaG
operon, encoding proteins of unknown function, among genes whose transcription is induced in response to nitrate, nitrite, or nitric oxide. Nitrate and nitrite regulate anaerobic respiratory gene expression through the NarX-NarL and NarQ-NarP two-component systems. All known Nar-activated genes also require the oxygen-responsive Fnr transcription activator. However, previous studies indicated that
yeaR-yoaG
operon transcription does not require Fnr activation. Here, we report results from mutational analyses demonstrating that
yeaR
-
yoaG
operon transcription is activated by phospho-NarL protein independent of the Fnr protein. The phospho-NarL protein binding site is centered at position −43.5 with respect to the transcription initiation site. Expression from the
Shewanella oneidensis
MR-1
nnrS
gene promoter, cloned into
E. coli
, similarly was activated by phospho-NarL protein independent of the Fnr protein. Recently,
yeaR-yoaG
operon transcription was shown to be regulated by the nitric oxide-responsive NsrR repressor (N. Filenko et al., J. Bacteriol. 189:4410-4417, 2007). Our mutational analyses reveal the individual contributions of the Nar and NsrR regulators to overall
yeaR-yoaG
operon expression and document the NsrR operator centered at position −32. Thus, control of
yeaR-yoaG
operon transcription provides an example of overlapping regulation by nitrate and nitrite, acting through the Nar regulatory system, and nitric oxide, acting through the NsrR repressor.
Cobalt Targets Multiple Metabolic Processes in
Salmonella enterica
Authors: Thorgersen Michael P. , Downs Diana M. 
Published: August 2007

ABSTRACT

Cobalt is essential for growth of
Salmonella enterica
and other organisms, yet this metal can be toxic when present in excess. Wild-type
Salmonella
exhibits several metabolic defects when grown in the presence of cobalt, some of which generate visible growth consequences. Work herein identifies sulfur assimilation, iron homeostasis, and Fe-S cluster metabolism as targets for cobalt toxicity. In each case it is proposed that cobalt exerts its effect by one of two mechanisms: direct competition with iron or indirectly through a mechanism that involves the status of reduced thiols in the cell. Cobalt toxicity results in decreased siroheme production, increased expression of the Fur regulon, and decreased activity of Fe-S cluster proteins. The consequences of reduced sulfite reductase activity in particular are exacerbated by the need for glutathione in cobalt resistance. Significantly, independent metabolic perturbations could be detected at cobalt concentrations below those required to generate a detectable growth defect.
Pyocin S2 (Sa) Kills
Pseudomonas aeruginosa
Strains via the FpvA Type I Ferripyoverdine Receptor
Authors: Denayer Sarah , Matthijs Sandra , Cornelis Pierre 
Published: August 2007

ABSTRACT

Soluble (S-type) pyocins are
Pseudomonas aeruginosa
bacteriocins that kill nonimmune
P. aeruginosa
strains via a specific receptor. The genes coding for pyocin Sa (consisting of a killing protein and an immunity protein) were cloned and expressed in
Escherichia coli
. Sequence analysis revealed that Sa is identical to pyocin S2. Seventy-nine strains of
P. aeruginosa
were tested for their sensitivity to pyocins S1, S2, and S3, and their ferripyoverdine receptors were typed by multiplex PCR. No strain was found to be sensitive to both S2 and S3, suggesting that the receptors for these two pyocins cannot coexist in one strain. As expected, all S3-sensitive strains had the type II ferripyoverdine receptor
fpvA
gene, confirming our previous reports. S1 killed strains irrespective of the type of ferripyoverdine receptor they produced. All S2-sensitive strains had the type I
fpvA
gene, and the inactivation of type I
fpvA
in an S2-sensitive strain conferred resistance to the S2 pyocin. Accordingly, complementation with type I
fpvA
in
trans
restored sensitivity to S2. Some S2-resistant type I
fpvA
-positive strains were detected, the majority (all but five) of which had the S1-S2 immunity gene. Comparison of type I
fpvA
sequences from immunity gene-negative S2-sensitive and S2-resistant strains revealed only a valine-to-isoleucine substitution at position 46 of type I FpvA. However, both type I
fpvA
genes conferred the capacity for type I pyoverdine utilization and sensitivity to S2. When these two type I
fpvA
genes were introduced into strain 7NSK2 carrying mutations in type II
fpvA
(encoding the type II pyoverdine receptor) and
fpvB
(encoding the alternative type I receptor), growth in the presence of type I pyoverdine was observed and the strain became sensitive to S2. We also found that type I pyoverdine could signal type II pyoverdine production via the type I FpvA receptor in 7NSK2.
Genome-Wide Transcriptional Changes inStreptococcus gordoniiin Response to Competence Signaling Peptide
Authors: Vickerman M. M. , Iobst S. , Jesionowski A. M. , Gill S. R. 
Published: August 2007

ABSTRACTStreptococcus gordoniiis a primary colonizer of the multispecies biofilm on tooth surfaces forming dental plaque and a potential agent of endocarditis. The recent completion of the genome sequence of the naturally competent strain Challis allowed the design of a spotted oligonucleotide microarray to examine a genome-wide response of this organism to environmental stimuli such as signal peptides. Based on temporal responses to synthetic competence signaling peptide (CSP) as indicated by transformation frequencies, theS. gordoniitranscriptome was analyzed at various time points after CSP exposure. Microarray analysis identified 35 candidate early genes and 127 candidate late genes that were up-regulated at 5 and 15 min, respectively; these genes were often grouped in clusters. Results supported published findings onS. gordoniicompetence, showing up-regulation of 12 of 16 genes that have been reported to affect transformation frequencies in this species. Comparison of CSP-inducedS. gordoniitranscriptomes to results published forStreptococcus pneumoniaestrains identified both conserved and species-specific genes. Putative intergenic regulatory sites, such as the conserved combox sequence thought to be a binding site for competence sigma factor, were found precedingS. gordoniilate responsive genes. In contrast,S. gordoniiearly CSP-responsive genes were not preceded by the direct repeats found inS. pneumoniae. These studies provide the first insights into a genome-wide transcriptional response of an oral commensal organism. They offer an extensive analysis of transcriptional changes that accompany competence inS. gordoniiand form a basis for future intra- and interspecies comparative analyses of this ecologically important phenotype.
Role of Sigma Factors in Controlling Global Gene Expression in Light/Dark Transitions in the CyanobacteriumSynechocystissp. Strain PCC 6803
Authors: Summerfield Tina C. , Sherman Louis A. 
Published: August 2007

ABSTRACTWe report on differential gene expression in the cyanobacteriumSynechocystissp. strain PCC 6803 after light-dark transitions in wild-type, ΔsigB, and ΔsigDstrains. We also studied the effect of day length in the presence of glucose on a ΔsigBΔsigEmutant. Our results indicated that the absence of SigB or SigD predominately altered gene expression in the dark or in the light, respectively. In the light, approximately 350 genes displayed transcript levels in the ΔsigDstrain that were different from those of the wild type, with over 200 of these up-regulated in the mutant. In the dark, removal of SigB altered more than 150 genes, and the levels of 136 of these were increased in the mutant compared to those in the wild type. The removal of both SigB and SigE had a major impact on gene expression under mixotrophic growth conditions and resulted in the inability of cells to grow in the presence of glucose with 8-h light and 16-h dark cycles. Our results indicated the importance of group II σ factors in the global regulation of transcription in this organism and are best explained by using the σ cycle paradigm with the stochastic release model described previously (R. A. Mooney, S. A. Darst, and R. Landick, Mol. Cell 20:335-345, 2005). We combined our results with the total protein levels of the σ factors in the light and dark as calculated previously (S. Imamura, S. Yoshihara, S. Nakano, N. Shiozaki, A. Yamada, K. Tanaka, H. Takahashi, M. Asayama, and M. Shirai, J. Mol. Biol.325:857-872, 2003; S. Imamura, M. Asayama, H. Takahashi, K. Tanaka, H. Takahashi, and M. Shirai, FEBS Lett.554:357-362, 2003). Thus, we concluded that the control of global transcription is based on the amount of the various σ factors present and able to bind RNA polymerase.
gerT
, a Newly Discovered Germination Gene under the Control of the Sporulation Transcription Factor σ
K
in
Bacillus subtilis
Authors: Ferguson Caitlin C. , Camp Amy H. , Losick Richard 
Published: August 2007

ABSTRACT

We report the identification of a gene, herein designated
gerT
(formerly
yozR
), that is involved in germination by spores of
Bacillus subtilis
. The
gerT
gene is induced late in sporulation under the positive control of the transcription factor σ
K
and under the negative control of the DNA-binding protein GerE. The
gerT
gene product (GerT) is a component of the spore coat, and its incorporation into the coat takes place in two stages. GerT initially assembles into foci, which then spread around the developing spore in a process that is dependent on the morphogenetic protein CotE. Mutant spores lacking GerT respond poorly to multiple germinants and are impaired at an early stage of germination.
Abh and AbrB Control of
Bacillus subtilis
Antimicrobial Gene Expression
Authors: Strauch Mark A. , Bobay Benjamin G. , Cavanagh John , Yao Fude , Wilson Angelo , Le Breton Yoann 
Published: August 2007

ABSTRACT

The
Bacillus subtilis abh
gene encodes a protein whose N-terminal domain has 74% identity to the DNA-binding domain of the global regulatory protein AbrB. Strains with a mutation in
abh
showed alterations in the production of antimicrobial compounds directed against some other
Bacillus
species and gram-positive microbes. Relative to its wild-type parental strain, the
abh
mutant was found deficient, enhanced, or unaffected for the production of antimicrobial activity. Using
lacZ
fusions, we examined the effects of
abh
upon the expression of 10 promoters known to be regulated by AbrB, including five that transcribe well-characterized antimicrobial functions (SdpC, SkfA, TasA, sublancin, and subtilosin). For an otherwise wild-type background, the results show that Abh plays a negative regulatory role in the expression of four of the promoters, a positive role for the expression of three, and no apparent regulatory role in the expression of the other three promoters. Binding of AbrB and Abh to the promoter regions was examined using DNase I footprinting, and the results revealed significant differences. The transcription of
abh
is not autoregulated, but it is subject to a degree of AbrB-afforded negative regulation. The results indicate that Abh is part of the complex interconnected regulatory system that controls gene expression during the transition from active growth to stationary phase.
Complex Regulation of Urease Formation from the Two Promoters of the
ure
Operon of
Klebsiella pneumoniae
Authors: Liu Qiong , Bender Robert A. 
Published: August 2007

ABSTRACT

Klebsiella pneumoniae
can use urea as the sole source of nitrogen, thanks to a urease encoded by the
ureDABCEFG
operon. Expression of this operon is independent of urea and is regulated by the supply of nitrogen in the growth medium. When cells were growth rate limited for nitrogen, the specific activity of urease was about 70 times higher than that in cells grown under conditions of excess nitrogen. Much of this nitrogen regulation of urease formation depended on the nitrogen regulatory system acting through the nitrogen assimilation control protein, NAC. In a strain deleted for the
nac
gene, nitrogen limitation resulted in only a 7-fold increase in the specific activity of urease, in contrast to the 70-fold increase seen in that of the wild type. The
ure
operon was transcribed from two promoters. The proximal promoter (P1) had an absolute requirement for NAC; little or no transcription was seen in the absence of NAC. The distal promoter (P2) was independent of NAC, but its activity increased about threefold when the growth rate of the cells was limited by the nitrogen source. Transcriptional regulation of P1 and P2 accounted for most of the changes in urease activity seen under various nitrogen conditions. However, when transcription of
ureDABCEFG
was less than 20% of its maximum, the amount of active urease formed per transcript of
ure
decreased almost linearly with decreasing transcription. This may reflect a defect in the assembly of active urease and accounted for as much as a threefold activity difference under the conditions tested here. Thus, the
ure
operon was transcribed from a NAC-independent promoter (P2) and the most strongly NAC-dependent promoter known (P1). Most of the regulation of urease formation was transcriptional, but when
ure
transcription was low, assembly of active urease also was defective.
Cloning of a Gene Cluster Involved in the Catabolism of
p
-Nitrophenol by
Arthrobacter
sp. Strain JS443 and Characterization of the
p
-Nitrophenol Monooxygenase
Authors: Perry Lynda L. , Zylstra Gerben J. 
Published: August 2007

ABSTRACT

The
npd
gene cluster, which encodes the enzymes of a
p
-nitrophenol catabolic pathway from
Arthrobacter
sp. strain JS443, was cloned and sequenced. Three genes,
npdB
,
npdA1
, and
npdA2
, were independently expressed in
Escherichia coli
in order to confirm the identities of their gene products. NpdA2 is a
p
-nitrophenol monooxygenase belonging to the two-component flavin-diffusible monooxygenase family of reduced flavin-dependent monooxygenases. NpdA1 is an NADH-dependent flavin reductase, and NpdB is a hydroxyquinol 1,2-dioxygenase. The
npd
gene cluster also includes a putative maleylacetate reductase gene,
npdC
. In an in vitro assay containing NpdA2, an
E. coli
lysate transforms
p
-nitrophenol stoichiometrically to hydroquinone and hydroxyquinol. It was concluded that the
p
-nitrophenol catabolic pathway in JS443 most likely begins with a two-step transformation of
p
-nitrophenol to hydroxy-1,4-benzoquinone, catalyzed by NpdA2. Hydroxy-1,4-benzoquinone is reduced to hydroxyquinol, which is degraded through the hydroxyquinol
ortho
cleavage pathway. The hydroquinone detected in vitro is a dead-end product most likely resulting from chemical or enzymatic reduction of the hypothetical intermediate 1,4-benzoquinone. NpdA2 hydroxylates a broad range of chloro- and nitro-substituted phenols, resorcinols, and catechols. Only
p
-nitro- or
p
-chloro-substituted phenols are hydroxylated twice. Other substrates are hydroxylated once, always at a position
para
to a hydroxyl group.
Physical examination tests of the shoulder: a systematic review with meta-analysis of individual tests
Authors: Hegedus E J , Goode A , Campbell S , Morin A , Tamaddoni M , Moorman C T , Cook C 
Published: August 2007

Objective:To compile and critique research on the diagnostic accuracy of individual orthopaedic physical examination tests in a manner that would allow clinicians to judge whether these tests are valuable to their practice.Methods:A computer-assisted literature search of MEDLINE, CINAHL, and SPORTDiscus databases (1966 to October 2006) using keywords related to diagnostic accuracy of physical examination tests of the shoulder. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool was used to critique the quality of each paper. Meta-analysis through meta-regression of the diagnostic odds ratio (DOR) was performed on the Neer test for impingement, the Hawkins−Kennedy test for impingement, and the Speed test for superior labral pathology.Results:Forty-five studies were critiqued with only half demonstrating acceptable high quality and only two having adequate sample size. For impingement, the meta-analysis revealed that the pooled sensitivity and specificity for the Neer test was 79% and 53%, respectively, and for the Hawkins−Kennedy test was 79% and 59%, respectively. For superior labral (SLAP) tears, the summary sensitivity and specificity of the Speed test was 32% and 61%, respectively. Regarding orthopaedic special tests (OSTs) where meta-analysis was not possible either due to lack of sufficient studies or heterogeneity between studies, the list that demonstrates both high sensitivity and high specificity is short: hornblowers’s sign and the external rotation lag sign for tears of the rotator cuff, biceps load II for superior labral anterior to posterior (SLAP) lesions, and apprehension, relocation and anterior release for anterior instability. Even these tests have been under-studied or are from lower quality studies or both. No tests for impingement or acromioclavicular (AC) joint pathology demonstrated significant diagnostic accuracy.Conclusion:Based on pooled data, the diagnostic accuracy of the Neer test for impingement, the Hawkins−Kennedy test for impingement and the Speed test for labral pathology is limited. There is a great need for large, prospective, well-designed studies that examine the diagnostic accuracy of the numerous physical examination tests of the shoulder. Currently, almost without exception, there is a lack of clarity with regard to whether common OSTs used in clinical examination are useful in differentially diagnosing pathologies of the shoulder.
Expression of HDAC1 and CBP/p300 in human colorectal carcinomas
Authors: Ishihama Katsuyoshi , Yamakawa Mitsunori , Semba Shuho , Takeda Hiroaki , Kawata Sumio , Kimura Seishi , Kimura Wataru 
Published: August 2007

Background:The histone-modifying enzymes histone deacetylase (HDAC) and histone acetyltransferase (HAT) control gene transcriptional activation and repression in human malignancies.Aims:To analyse the expression of HDAC/HAT-associated molecules such as HDAC1, CREB-binding protein (CBP) and p300 in human colorectal carcinomas, and investigate the relationship between their expression levels and clinicopathological parameters.Methods:Expression levels of HDAC1, CBP, and p300 in human colorectal cancer were investigated by immunohistochemistry. In situ hybridisation (ISH) and reverse transcription (RT)-PCR analyses were also carried out to confirm mRNA expression levels of these genes. Immunoreactivity was evaluated semi-quantitatively using a staining index (SI). The relationships between the SIs and clinicopathological findings were analysed and survival curves were calculated using the Kaplan–Meier method and log-rank tests.Results:The mean SIs for HDAC1, CBP, and p300 in this series of tumours were much higher than those in normal colonic mucosa. The presence ofHDAC1andCBPmRNAs on colorectal carcinoma cells as well as normal epithelial cells was confirmed by ISH analysis. A marked increase inp300mRNA levels was detected in a majority of cases by RT-PCR. Among the patients with colorectal cancer, overexpression of p300 (SI>11.9) correlated with a poor prognosis, whereas high CBP expression levels (SI>16.6) indicated long-term survival.Conclusion:Results showed the up-regulation of these three histone-modifying molecules in this series of colorectal cancers and suggested that monitoring of CBP and p300 may assist prediction of the prognosis in patients with colorectal adenocarcinoma.