bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Functional Identity for the DNA Uptake Sequence in Transformation and Its Presence in Transcriptional Terminators
Authors: Ambur O. Herman , Frye Stephan A. , Tønjum Tone 
Published: December 2006

ABSTRACT

The frequently occurring DNA uptake sequence (DUS), recognized as a 10-bp repeat, is required for efficient genetic transformation in the human pathogens
Neisseria meningitidis
and
Neisseria gonorrhoeae
. Genome scanning for DUS occurrences in three different species of
Neisseria
demonstrated that 76% of the nearly 2,000 neisserial DUS were found to have two semiconserved base pairs extending from the 5′ end of DUS to constitute a 12-mer repeat. Plasmids containing sequential variants of the neisserial DUS were tested for their ability to transform
N. meningitidis
and
N. gonorrhoeae
, and the 12-mer was found to outperform the 10-mer DUS in transformation efficiency. Assessment of meningococcal uptake of DNA confirmed the enhanced performance of the 12-mer compared to the 10-mer DUS. An inverted repeat DUS was not more efficient in transformation than DNA species containing a single or direct repeat DUS. Genome-wide analysis revealed that half of the nearly 1,500 12-mer DUS are arranged as inverted repeats predicted to be involved in rho-independent transcriptional termination or attenuation. The distribution of the uptake signal sequence required for transformation in the
Pasteurellaceae
was also biased towards transcriptional terminators, although to a lesser extent. In addition to assessing the intergenic location of DUS, we propose that the 10-mer identity of DUS should be extended and recognized as a 12-mer DUS. The dual role of DUS in transformation and as a structural component on RNA affecting transcription makes this a relevant model system for assessing significant roles of repeat sequences in biology.
Complete and SOS-Mediated Response of
Staphylococcus aureus
to the Antibiotic Ciprofloxacin
Authors: Cirz Ryan T. , Jones Marcus B. , Gingles Neill A. , Minogue Timothy D. , Jarrahi Behnam , Peterson Scott N. , Romesberg Floyd E. 
Published: December 2006

ABSTRACT

Staphylococcus aureus
infections can be difficult to treat due to both multidrug resistance and the organism's remarkable ability to persist in the host. Persistence and the evolution of resistance may be related to several complex regulatory networks, such as the SOS response, which modifies transcription in response to environmental stress. To understand how
S. aureus
persists during antibiotic therapy and eventually emerges resistant, we characterized its global transcriptional response to ciprofloxacin. We found that ciprofloxacin induces prophage mobilization as well as significant alterations in metabolism, most notably the up-regulation of the tricarboxylic acid cycle. In addition, we found that ciprofloxacin induces the SOS response, which we show, by comparison of a wild-type strain and a non-SOS-inducible
lexA
mutant strain, includes the derepression of 16 genes. While the SOS response of
S. aureus
is much more limited than those of
Escherichia coli
and
Bacillus subtilis
, it is similar to that of
Pseudomonas aeruginosa
and includes RecA, LexA, several hypothetical proteins, and a likely error-prone Y family polymerase whose homologs in other bacteria are required for induced mutation. We also examined induced mutation and found that either the inability to derepress the SOS response or the lack of the LexA-regulated polymerase renders
S. aureus
unable to evolve antibiotic resistance in vitro in response to UV damage. The data suggest that up-regulation of the tricarboxylic acid cycle and induced mutation facilitate
S. aureus
persistence and evolution of resistance during antibiotic therapy.
Substrate Specificity of the
Escherichia coli
Outer Membrane Protease OmpP
Authors: Hwang Bum-Yeol , Varadarajan Navin , Li Haixin , Rodriguez Sarah , Iverson Brent L. , Georgiou George 
Published: December 2006

ABSTRACT

Escherichia coli
OmpP is an F episome-encoded outer membrane protease that exhibits 71% amino acid sequence identity with OmpT. These two enzymes cleave substrate polypeptides primarily between pairs of basic amino acids. We found that, like OmpT, purified OmpP is active only in the presence of lipopolysaccharide. With optimal peptide substrates, OmpP exhibits high catalytic efficiency (
k
cat
/

K
m

= 3.0 × 10
6
M
−1
s
−1
). Analysis of the extended amino acid specificity of OmpP by substrate phage revealed that both Arg and Lys are strongly preferred at the P1 and P1′ sites of the enzyme. In addition, Thr, Arg, or Ala is preferred at P2; Leu, Ala, or Glu is preferred at P4; and Arg is preferred at P3′. Notable differences in OmpP and OmpT specificities include the greater ability of OmpP to accept Lys at the P1 or P1′, site as well as the prominence of Ser at P3 in OmpP substrates. Likewise, the OmpP P1 site could better accommodate Ser; as a result, OmpP was able to cleave a peptide substrate between Ser-Arg about 120 times more efficiently than was OmpT. Interestingly, OmpP and OmpT cleave peptides with three consecutive Arg residues at different sites, a difference in specificity that might be important in the inactivation of cationic antimicrobial peptides. Accordingly, we show that the presence of an F′ episome results in increased resistance to the antimicrobial peptide protamine both in
ompT
mutants and in wild-type
E. coli
cells.
Escherichia coli
HdeB Is an Acid Stress Chaperone
Authors: Kern Renée , Malki Abderrahim , Abdallah Jad , Tagourti Jihen , Richarme Gilbert 
Published: December 2006

ABSTRACT

We cloned, expressed, and purified the
hdeB
gene product, which belongs to the
hdeAB
acid stress operon. We extracted HdeB from bacteria by the osmotic-shock procedure and purified it to homogeneity by ion-exchange chromatography and hydroxyapatite chromatography. Its identity was confirmed by mass spectrometry analysis. HdeB has a molecular mass of 10 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, which matches its expected molecular mass. We purified the acid stress chaperone HdeA in parallel in order to compare the two chaperones. The
hdeA
and
hdeB
mutants both display reduced viability upon acid stress, and only the HdeA/HdeB expression plasmid can restore their viability to close to the wild-type level, suggesting that both proteins are required for optimal protection of the bacterial periplasm against acid stress. Periplasmic extracts from both mutants aggregate at acidic pH, suggesting that HdeA and HdeB are required for protein solubilization. At pH 2, the aggregation of periplasmic extracts is prevented by the addition of HdeA, as previously reported, but is only slightly reduced by HdeB. At pH 3, however, HdeB is more efficient than HdeA in preventing periplasmic-protein aggregation. The solubilization of several model substrate proteins at acidic pH supports the hypothesis that, in vitro, HdeA plays a major role in protein solubilization at pH 2 and that both proteins are involved in protein solubilization at pH 3. Like HdeA, HdeB exposes hydrophobic surfaces at acidic pH, in accordance with the appearance of its chaperone properties at acidic pH. HdeB, like HdeA, dissociates from dimers at neutral pH into monomers at acidic pHs, but its dissociation is complete at pH 3 whereas that of HdeA is complete at a more acidic pH. Thus, we can conclude that
Escherichia coli
possesses two acid stress chaperones that prevent periplasmic-protein aggregation at acidic pH.
Expression of the Iron-ActivatednspAandsecYGenes inNeisseria meningitidisGroup B by Fur-Dependent and -Independent Mechanisms
Authors: Shaik Yazdani B. , Grogan Susan , Davey Michael , Sebastian Shite , Goswami Sulip , Szmigielski Borys , Genco Caroline A. 
Published: December 2006

ABSTRACTOur whole-genome microarray studies ofNeisseria meningitidisMC58 previously identified a set of 153 genes whose transcription was activated during growth in iron. In this study, Fur-mediated regulation of the iron-activatednspAgene was confirmed, whereas iron-activated regulation of thesecYgene was demonstrated to be Fur independent. Analysis of the Fur binding sequences in thenspAgene and an additional iron-activated and Fur-regulated gene identified a hexameric (G/T)ATAAT unit in the operator regions of these genes similar to that observed in Fur- and iron-repressed genes. These studies indicate that the expression of the iron-activatednspAandsecYgenes inN. meningitidisoccur by Fur-dependent and -independent mechanisms, respectively.
Diversity of the Abundant pKLC102/PAGI-2 Family of Genomic Islands inPseudomonas aeruginosa
Authors: Klockgether Jens , Würdemann Dieco , Reva Oleg , Wiehlmann Lutz , Tümmler Burkhard 
Published: December 2006

ABSTRACTThe known genomic islands ofPseudomonas aeruginosaclone C strains are integrated into tRNALys(pKLC102) or tRNAGly(PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 fromP. aeruginosaPA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelatedP. aeruginosastrains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequentialP. aeruginosaisolates from individuals with cystic fibrosis. PAGI-2 was present in most testedCupriavidus metalliduransandCupriavidus campinensisisolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.
Comparison between Nasal Swabs and Nasopharyngeal Aspirates for, and Effect of Time in Transit on, Isolation of
Streptococcus pneumoniae
,
Staphylococcus aureus
,
Haemophilus influenzae
, and
Moraxella catarrhalis
Authors: Carville Kylie S. , Bowman Jacinta M. , Lehmann Deborah , Riley Thomas V. 
Published: December 2006

ABSTRACT

We assessed the impact of the use of nasal swabs or nasopharyngeal aspirates and the time from specimen collection to storage at −70°C on bacterial isolation.
Haemophilus influenzae
was isolated significantly less often from swabs than from nasopharyngeal aspirates. Samples in transit for >3 days were half as likely to grow
Streptococcus pneumoniae
and
H. influenzae
as those in transit for ≤3 days. There was no statistically significant difference for either
Moraxella catarrhalis
or
Staphylococcus aureus
.
Assessment of an Optimized Mycobacterial Interspersed Repetitive- Unit-Variable-Number Tandem-Repeat Typing System Combined with Spoligotyping for Population-Based Molecular Epidemiology Studies of Tuberculosis
Authors: Oelemann Mara Cardoso , Diel Roland , Vatin Vincent , Haas Walter , Rüsch-Gerdes Sabine , Locht Camille , Niemann Stefan , Supply Philip 
Published: December 2006

ABSTRACTAn optimized set of 24 mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) loci, including a discriminatory subset of 15 loci, has recently been defined for the typing ofMycobacterium tuberculosis. Here, we evaluated the performances of this MIRU-VNTR typing system in combination with spoligotyping for the detection of transmission chains in a population-based study comprising 91% of culture-confirmed tuberculosis patients reported in 2003 in Hamburg, Germany. Of the 154 isolates investigated, more than 90% had high IS6110copy numbers (≥6). IS6110restriction fragment length polymorphism (RFLP) typing resulted in 13 clusters, 5 of which had a confirmed epidemiological link. All five, as well as six of the eightIS6110clusters with no identified epidemiological link, were perfectly matched by MIRU-VNTR typing with the 24 loci. Two IS6110clusters were split by differences into 6 to 12 MIRU-VNTR loci, clearly supporting the absence of a link, as judged by contact tracing data. In contrast, only one MIRU-VNTR cluster, grouping what were probably epidemiologically unlinked isolates, was split by IS6110RFLP. However, these isolates were also distinguished by spoligotyping. Both the optimized 24-locus and 15-locus sets thus showed a comparable to slightly better predictive value, especially when combined with spoligotyping, than the current gold standard IS6110RFLP for the study of tuberculosis transmission in Hamburg. Because the epidemiological characteristics of this setting are similar to those of many developed countries, these results support the wide applicability of this real-time genotyping approach for population-based studies ofM. tuberculosistransmission.
tcdC
Genotypes Associated with Severe TcdC Truncation in an Epidemic Clone and Other Strains of
Clostridium difficile
Authors: Curry Scott R. , Marsh Jane W. , Muto Carlene A. , O'Leary Mary M. , Pasculle A. William , Harrison Lee H. 
Published: December 2006

ABSTRACT

Severe
Clostridium difficile
associated disease is associated with outbreaks of the recently described BI/NAP1 epidemic clone. This clone is characterized by an 18-bp deletion in the
tcdC
gene and increased production of toxins A and B in vitro. TcdC is a putative negative regulator of toxin A&B production. We characterized
tcdC
genotypes from a collection of
C. difficile
isolates from a hospital that experienced an outbreak caused by the BI/NAP1 epidemic clone. Sequence analysis of
tcdC
was performed on DNA samples isolated from 199 toxigenic
C. difficile
isolates (31% BI/NAP1) from 2001 and 2005. Sequences obtained from 36 (18.6%) isolates predicted wild-type TcdC (232 amino acid residues), whereas 12 (6.1%) isolates had
tcdC
genotypes with previously described 18- or 39-bp deletions. The remaining isolates comprised 15 unique genotypes. Of these, 5 genotypes contain 18- or 36-bp deletions. Of these five genotypes, one is characterized by a single nucleotide deletion at position 117 resulting in a frameshift that introduces a stop codon at position 196, truncating the predicted TcdC to 65 amino acid residues. All 62 of the isolates in this collection comprising the epidemic clone are characterized by this genotype. This result suggests that severe truncation of TcdC is responsible for the increased toxin production observed in strains belonging to the BI/NAP1 clone and that the 18-bp deletion is probably irrelevant to TcdC function. Further investigations are required to determine the effect of this and other
tcd
C genotypes on toxin production and clinical disease.
Staphylococcal Cassette Chromosome
mec
and Panton-Valentine Leukocidin Characterization of Methicillin-Resistant
Staphylococcus aureus
Clones
Authors: Moroney Shannon M. , Heller Loree C. , Arbuckle Jesse , Talavera Monica , Widen Ray H. 
Published: December 2006

ABSTRACT

Staphylococcal cassette chromosome
mec
(SCC
mec
) types and Panton-Valentine leukocidin (PVL) gene carriage were compared among suspected community-associated methicillin-resistant
Staphylococcus aureus
MRSA (CA-MRSA) and health care-associated MRSA (HA-MRSA) isolates. CA-MRSA isolates carried the SCC
mec
type IV complex, and most were PVL positive. The HA-MRSA isolates carried the SCC
mec
type II complex and did not harbor the PVL genes.
Genotypic Analysis of Invasive
Streptococcus pneumoniae
from Mali, Africa, by Semiautomated Repetitive-Element PCR and Pulsed-Field Gel Electrophoresis
Authors: Harrington S. M. , Stock F. , Kominski A. L. , Campbell J. D. , Hormazabal J. C. , Livio S. , Rao L. , Kotloff K. L. , Sow S. O. , Murray P. R. 
Published: December 2006

ABSTRACT

As part of a large, ongoing study of invasive infections in pediatric patients in Bamako, Mali, 106 cases of invasive pneumococcal disease were identified from June 2002 to July 2003 (J. D. Campbell et al., Pediatr. Infect. Dis. J. 23:642-649, 2004). Of the 12 serotypes present, the majority of isolates were not contained in PCV7 (the 7-valent pneumococcal conjugate vaccine), including 1 isolate that was serotype 1, 12 isolates that were serotype 2, 58 isolates that were serotype 5, 7 isolates that were serotype 7F, and 1 isolate that was serotype 12F. To determine whether clonal dissemination of the predominant serotypes had taken place, genotyping was performed on 100
S. pneumoniae
isolates by using two methods: pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA, and the Bacterial Barcodes repetitive-element PCR (rep-PCR) method. Criteria for delineating rep-PCR genotypes were established such that isolates of different serotypes were generally not grouped together. The two methods were equally discriminatory within a given pneumococcal serotype. PFGE separated the isolates into 15 genotypes and 7 subtypes; rep-PCR separated isolates into 15 genotypes and 6 subtypes. Using either method, isolates within serotypes 2, 5, and 7 formed three large, separate clusters containing 1 genotype each. Both methods further distinguished related subtypes within serotypes 2 and 5. Interestingly, one of the PFGE subtypes of serotype 5 is indistinguishable from the Columbia
5
-19 clone circulating in Latin America since 1994. The data support that serotypes 2 and 5 were likely to be the result of dissemination of particular clones, some of which are responsible for invasive disease over a broad population range.
Identification and Characterization of Peptides That Interact with Hepatitis B Virus via the Putative Receptor Binding Site
Authors: Deng Qiang , Zhai Jian-wei , Michel Marie-Louise , Zhang Jun , Qin Jun , Kong Yu-ying , Zhang Xin-xin , Budkowska Agata , Tiollais Pierre , Wang Yuan , Xie You-hua 
Published: December 2006

ABSTRACT

A direct involvement of the PreS domain of the hepatitis B virus (HBV) large envelope protein, and in particular amino acid residues 21 to 47, in virus attachment to hepatocytes has been suggested by many previous studies. Several PreS-interacting proteins have been identified. However, they share few common sequence motifs, and a bona fide cellular receptor for HBV remains elusive. In this study, we aimed to identify PreS-interacting motifs and to search for novel HBV-interacting proteins and the long-sought receptor. PreS fusion proteins were used as baits to screen a phage display library of random peptides. A group of PreS-binding peptides were obtained. These peptides could bind to amino acids 21 to 47 of PreS1 and shared a linear motif (W
1
T
2
X
3
W
4
W
5
) sufficient for binding specifically to PreS and viral particles. Several human proteins with such a motif were identified through BLAST search. Analysis of their biochemical and structural properties suggested that lipoprotein lipase (LPL), a key enzyme in lipoprotein metabolism, might interact with PreS and HBV particles. The interaction of HBV with LPL was demonstrated by in vitro binding, virus capture, and cell attachment assays. These findings suggest that LPL may play a role in the initiation of HBV infection. Identification of peptides and protein ligands corresponding to LPL that bind to the HBV envelope will offer new therapeutic strategies against HBV infection.
Conserved Determinants for Membrane Association of Nonstructural Protein 5A fromHepatitis C Virus and Related Viruses
Authors: Brass Volker , Pal Zsuzsanna , Sapay Nicolas , Deléage Gilbert , Blum Hubert E. , Penin François , Moradpour Darius 
Published: December 2006

ABSTRACT

Nonstructural protein 5A (NS5A) is a membrane-associated essential component of the hepatitis C virus (HCV) replication complex. An N-terminal amphipathic
alpha helix mediates in-plane membrane association of HCV NS5A and at
the same time is likely involved in specific protein-protein
interactions required for the assembly of a functional replication
complex. The aim of this study was to identify the determinants for
membrane association of NS5A from the related GB viruses and
pestiviruses. Although primary amino acid sequences differed
considerably, putative membrane anchor domains with amphipathic
features were predicted in the N-terminal domains of NS5A proteins from
these viruses. Confocal laser scanning microscopy, as well as membrane
flotation analyses, demonstrated that NS5As from GB virus B (GBV-B),
GBV-C, and bovine viral diarrhea virus, the prototype pestivirus,
display membrane association characteristics very similar to those of
HCV NS5A. The N-terminal 27 to 33 amino acid residues of these NS5A
proteins were sufficient for membrane association. Circular dichroism
analyses confirmed the capacity of these segments to fold into alpha
helices upon association with lipid-like molecules. Despite structural
conservation, only very limited exchanges with sequences from related
viruses were tolerated in the context of functional HCV RNA
replication, suggesting virus-specific interactions of these segments.
In conclusion, membrane association of NS5A by an N-terminal
amphipathic alpha helix is a feature shared by HCV and related members
of the family
Flaviviridae
. This observation points to
conserved roles of the N-terminal amphipathic alpha helices of NS5A in
replication complex
formation.
Cytomegalovirus Primary Envelopment Occurs at Large Infoldings of the Inner Nuclear Membrane
Authors: Buser Christopher , Walther Paul , Mertens Thomas , Michel Detlef 
Published: December 2006

ABSTRACTWe have investigated the morphogenesis of human and murine cytomegalovirus by transmission electron microscopy after high-pressure freezing, freeze substitution, and plastic embedding. We observed large tubular infoldings of the inner nuclear membrane that were free of lamina and active in primary envelopment and subsequent transport of capsids to the nuclear periphery. Semiquantitative determinations of the enlarged inner nuclear membrane area and the location of the primary envelopment of nucleocapsids demonstrated that this structure represents a virus-induced specialized membrane domain at which the particles are preferentially enveloped. This is a previously undescribed structural element relevant in cytomegalovirus morphogenesis.
Oncolytic Vesicular Stomatitis Virus Induces Apoptosis via Signaling through PKR, Fas, and Daxx
Authors: Gaddy Daniel F. , Lyles Douglas S. 
Published: December 2006

ABSTRACT
Matrix (M) protein mutants of vesicular stomatitis virus (VSV) are promising oncolytic agents for cancer therapy. Previous research has implicated Fas and PKR in apoptosis induced by other viruses. Here, we show that dominant-negative mutants of Fas and PKR inhibit M protein mutant virus-induced apoptosis. Most previous research has focused on the adapter protein FADD as a necessary transducer of Fas-mediated apoptosis. However, the expression of dominant-negative FADD had little effect on the induction of apoptosis by M protein mutant VSV. Instead, virus-induced apoptosis was inhibited by the expression of a dominant-negative mutant of the adapter protein Daxx. These data indicate that Daxx is more important than FADD for apoptosis induced by M protein mutant VSV. These results show that PKR- and Fas-mediated signaling play important roles in cell death during M protein mutant VSV infection and that Daxx has novel functions in the host response to virus infection by mediating virus-induced apoptosis.