bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Regulation ofBacillus subtilis phoPRTranscription by Transition State Regulator ScoC
Authors: Kaushal Bindiya , Paul Salbi , Hulett F. Marion 
Published: April 2010

ABSTRACTInduction of the Pho response inBacillus subtilisoccurs when the Piconcentrations in the growth medium fall below 0.1 mM, a condition which results in slowed cellular growth followed by entry into stationary phase. ThephoPRpromoter region contains three σA-responsive promoters; only promoter PA4is PhoP autoregulated. Expression of thephoPRoperon is postexponential, suggesting the possibility of a repressor role for a transition-state-regulatory protein(s). Expression of aphoPRpromoter-lacZfusion in ascoCloss-of-function mutant strain grown in low-phosphate defined medium was significantly higher than expression in the wild-type strain during exponential growth or stationary phase. Derepression in thescoCstrain from aphoPpromoter fusion containing a mutation in the CcpA binding site (cre1) was further elevated approximately 1.4-fold, indicating that the repressor effects of ScoC and CcpA onphoPexpression were cumulative. DNase I footprinting showed protection of putative binding sites by ScoC, which included the −10 and/or −35 elements of five (PB1, PE2, PA3, PA4, and PA6) of the six promoters within thephoPRpromoter region. PA6was expressedin vivofrom thephoP cre1promoter fusion in both wild-type andscoCstrains. Evidence for ScoC repressionin vivowas shown by primer extension for PA4and PA3from the wild-type promoter and for PA4and PE2from thephoP cre1promoter. The latter may reflect ScoC repression of sporulation that indirectly affectsphoPRtranscription. ScoC was shown to repress PA6, PA4, PE2, and PB1in vitro.
A Solvent-Exposed Patch in Chaperone-Bound YopE Is Required for Translocation by the Type III Secretion System
Authors: Rodgers Loren , Mukerjea Romila , Birtalan Sara , Friedberg Devorah , Ghosh Partho 
Published: April 2010

ABSTRACT

Most effector proteins of bacterial type III secretion (T3S) systems require chaperone proteins for translocation into host cells. Such effectors are bound by chaperones in a conserved and characteristic manner, with the chaperone-binding (Cb) region of the effector wound around the chaperone in a highly extended conformation. This conformation has been suggested to serve as a translocation signal in promoting the association between the chaperone-effector complex and a bacterial component required for translocation. We sought to test a prediction of this model by identifying a potential association site for the
Yersinia pseudotuberculosis
chaperone-effector pair SycE-YopE. We identified a set of residues in the YopE Cb region that are required for translocation but are dispensable for expression, SycE binding, secretion into the extrabacterial milieu, and stability in mammalian cells. These residues form a solvent-exposed patch on the surface of the chaperone-bound Cb region, and thus their effect on translocation is consistent with the structure of the chaperone-bound Cb region serving as a signal for translocation.
Loss of the WaaL O-Antigen Ligase Prevents Surface Activation of the Flagellar Gene Cascade in
Proteus mirabilis
Authors: Morgenstein Randy M. , Clemmer Katy M. , Rather Philip N. 
Published: April 2010

ABSTRACT

Proteus mirabilis
is a Gram-negative bacterium that undergoes a physical and biochemical change from a vegetative swimmer cell (a typical Gram-negative rod) to an elongated swarmer cell when grown on a solid surface. In this study, we report that a transposon insertion in the
waaL
gene, encoding O-antigen ligase, blocked swarming motility on solid surfaces but had little effect on swimming motility in soft agar. The
waaL
mutant was unable to differentiate into a swarmer cell. Differentiation was also prevented by a mutation in
wzz
, encoding a chain length determinant for O antigen, but not by a mutation in
wzyE
, encoding an enzyme that polymerizes enterobacterial common antigen, a surface polysaccharide different from the lipid A::core. In wild-type
P. mirabilis
, increased expression of the
flhDC
operon occurs after growth on solid surfaces and is required for the high-level expression of flagellin that is characteristic of swarmer cells. However, in both the
waaL
and the
wzz
mutants, the
flhDC
operon was not activated during growth on agar. A loss-of-function mutation in the
rcsB
response regulator or overexpression of
flhDC
restored swarming to the
waaL
mutant, despite the absence of O antigen. Therefore, although O antigen may serve a role in swarming by promoting wettability, the loss of O antigen blocks a regulatory pathway that links surface contact with the upregulation of
flhDC
expression.
A Highly Selective Oligopeptide Binding Protein from the Archaeon
Sulfolobus Solfataricus
Authors: Gogliettino M. , Balestrieri M. , Pocsfalvi G. , Fiume I. , Natale L. , Rossi M. , Palmieri G. 
Published: April 2010

ABSTRACT

SSO1273 of
Sulfolobus solfataricus
was identified as a cell surface-bound protein by a proteomics approach. Sequence inspection of the genome revealed that the open reading frame of
sso1273
is associated in an operon-like structure with genes encoding all the remaining components of a canonical protein-dependent ATP-binding cassette (ABC) transporter.
sso1273
gene expression and SSO1273 protein accumulation on the cell surface were demonstrated to be strongly induced by the addition of a peptide mixture (tryptone) to the culture medium. The native protein was obtained in multimeric form, mostly hexameric, under the purification conditions used, and it was characterized as an oligopeptide binding protein, named
S. solfataricus
OppA (OppA
Ss
). OppaA
Ss
possesses typical sequence patterns required for glycosylphosphatidylinositol lipid anchoring, resulting in an N-linked glycoprotein with carbohydrate moieties likely composed of high mannose and/or hybrid complex carbohydrates. OppA
Ss
specifically binds oligopeptides and shows a marked selectivity for the amino acid composition of substrates when assayed in complex peptide mixtures. Moreover, a truncated version of OppA
Ss
, produced in recombinant form and including the putative binding domain, showed a low but significant oligopeptide binding activity.
Roles of CcrA and CcrB in Excision and Integration of Staphylococcal Cassette Chromosome
mec
, a
Staphylococcus aureus
Genomic Island
Authors: Wang Lei , Archer Gordon L. 
Published: April 2010

ABSTRACT

The gene encoding resistance to methicillin and other β-lactam antibiotics in staphylococci,
mecA
, is carried on a genomic island, SCC
mec
(for staphylococcal cassette chromosome
mec
). The chromosomal excision and integration of types I to IV SCC
mec
are catalyzed by the site-specific recombinases CcrA and CcrB, the genes for which are encoded on each element. We sought to identify the relative contributions of CcrA and CcrB in the excision and integration of SCC
mec
. Purified CcrB but not CcrA was shown to mediate the gel shift of chromosomal target integration sequences (
attB
) in electrophoretic mobility shift assays. However, preincubation of CcrB-DNA complexes with increasing concentrations of CcrA blocked gel shift. The interaction of CcrB and CcrA was confirmed by
Escherichia coli
two-hybrid analysis. SCC
mec
excision mediated by plasmid-encoded and inducible
ccrA
,
ccrB
, or both genes was assessed by PCR in
Staphylococcus aureus
. CcrB alone could mediate excision but excision was at an alternate
att
site (
attR2
) within the right extremity of SCC
mec
. In contrast, both CcrB and CcrA were required to mediate excision at the chromosomal
attB
site (called
attR
when SCC
mec
is integrated). Insertion of a plasmid containing the SCC
mec att
site (
attS
) into the chromosome required both CcrA and CcrB, but CcrA overexpression lowered integration frequency. Thus, while CcrB binds DNA, interaction between CcrA and CcrB, in a precise ratio, is required for
attB
site-specific excision and SCC
mec
chromosomal insertion.
Lumbar Tuberculosis Associated with Membranous Nephropathy and Interstitial Nephritis
Authors: Yuan Quan , Sun Li , Feng Jiangmin , Liu Nan , Jiang Yi , Ma Jianfei , Wang Lining 
Published: April 2010

ABSTRACT
Tuberculosis is a common disease worldwide. However, it now is clear that tuberculosis can affect the kidney more insidiously. We describe a case of lumbar tuberculosis associated with simultaneous membranous nephropathy and interstitial nephritis, in which recovery of renal function occurred after treatment with steroids in addition to antituberculosis agents.
Molecular Detection and Identification of
Zygomycetes
Species from Paraffin-Embedded Tissues in a Murine Model of Disseminated Zygomycosis: a Collaborative European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Fungal Infection Study Group (EFISG) Evaluation
Authors: Dannaoui Eric , Schwarz Patrick , Slany Michal , Loeffler Juergen , Jorde Anne Tomine , Cuenca-Estrella Manuel , Hauser Philippe M. , Shrief Raghdaa , Huerre Michel , Freiberger Tomas , Gaustad Peter , Rodriguez-Tudela Juan-Luis , Bille Jacques , Denning David W. , Bretagne Stéphane , Lortholary Olivier 
Published: April 2010

ABSTRACT

The present study was performed to assess the interlaboratory reproducibility of the molecular detection and identification of species of
Zygomycetes
from formalin-fixed paraffin-embedded kidney and brain tissues obtained from experimentally infected mice. Animals were infected with one of five species (
Rhizopus oryzae
,
Rhizopus microsporus
,
Lichtheimia corymbifera
,
Rhizomucor pusillus
, and
Mucor circinelloides
). Samples with 1, 10, or 30 slide cuts of the tissues were prepared from each paraffin block, the sample identities were blinded for analysis, and the samples were mailed to each of seven laboratories for the assessment of sensitivity. A protocol describing the extraction method and the PCR amplification procedure was provided. The internal transcribed spacer 1 (ITS1) region was amplified by PCR with the fungal universal primers ITS1 and ITS2 and sequenced. As negative results were obtained for 93% of the tissue specimens infected by
M. circinelloides
, the data for this species were excluded from the analysis. Positive PCR results were obtained for 93% (52/56), 89% (50/56), and 27% (15/56) of the samples with 30, 10, and 1 slide cuts, respectively. There were minor differences, depending on the organ tissue, fungal species, and laboratory. Correct species identification was possible for 100% (30 cuts), 98% (10 cuts), and 93% (1 cut) of the cases. With the protocol used in the present study, the interlaboratory reproducibility of ITS sequencing for the identification of major
Zygomycetes
species from formalin-fixed paraffin-embedded tissues can reach 100%, when enough material is available.
Cyclomodulins in Urosepsis Strains of
Escherichia coli
Authors: Dubois Damien , Delmas Julien , Cady Anne , Robin Frédéric , Sivignon Adeline , Oswald Eric , Bonnet Richard 
Published: April 2010

ABSTRACT

Determinants of urosepsis in
Escherichia coli
remain incompletely defined. Cyclomodulins (CMs) are a growing functional family of toxins that hijack the eukaryotic cell cycle. Four cyclomodulin types are actually known in
E. coli
: cytotoxic necrotizing factors (CNFs), cycle-inhibiting factor (Cif), cytolethal distending toxins (CDTs), and the
pks
-encoded toxin. In the present study, the distribution of CM-encoding genes and the functionality of these toxins were investigated in 197
E. coli
strains isolated from patients with community-acquired urosepsis (
n
= 146) and from uninfected subjects (
n
= 51). This distribution was analyzed in relation to the phylogenetic background, clinical origin, and antibiotic resistance of the strains. It emerged from this study that strains harboring the
pks
island and the
cnf1
gene (i) were strongly associated with the B2 phylogroup (
P
, <0.001), (ii) frequently harbored both toxin-encoded genes in phylogroup B2 (33%), and (iii) were predictive of a urosepsis origin (
P
, <0.001 to 0.005). However, the prevalences of the
pks
island among phylogroup B2 strains, in contrast to those of the
cnf1
gene, were not significantly different between fecal and urosepsis groups, suggesting that the
pks
island is more important for the colonization process and the
cnf1
gene for virulence.
pks
-
or cnf1
-harboring strains were significantly associated with susceptibility to antibiotics (amoxicillin, cotrimoxazole, and quinolones [
P
, <0.001 to 0.043]). Otherwise, only 6% and 1% of all strains harbored the
cdtB
and
cif
genes, respectively, with no particular distribution by phylogenetic background, antimicrobial susceptibility, or clinical origin.
Use of Luminescent
Leptospira interrogans
for Enumeration in Biological Assays
Authors: Murray Gerald L. , King Amy M. , Srikram Amporn , Sermswan Rasana W. , Adler Ben 
Published: April 2010

ABSTRACT

Rapid and reliable
in vitro
methods for the detection of pathogenic leptospires, such as
Leptospira interrogans
, are lacking. The present study investigated the use of luminescence to replace the existing enumeration techniques. Transposon Tn
SC189
was modified to incorporate the
luxCDABE
cassette from
Photorhabdus luminescens
and was used to construct luminescent
Leptospira
spp. There was a linear relationship between luminescence and cell number, with the theoretical detection limit being less than 10
4
leptospires. A comparison of enumeration by a standard method (counting by dark-field microscopy) and enumeration by luminescence was conducted with luminescent
L. interrogans
. There was a good correlation between the two methods of enumeration (
R
2
= 0.766), although variation in the luminescence early and late in growth phase reduced the degree of correlation. To demonstrate the utility of luminescence as a viability and cell number reporter,
in vitro
assays, including MIC determination, an extracellular matrix binding experiment, and a complement killing experiment, were conducted. In each case, the results obtained by luminescence matched those obtained by traditional means with high correlations (binding assay
R
2
= 0.916, complement killing assay
R
2
= 0.988). A strain expressing the
luxCDABE
transposon retained virulence in the hamster model of infection. Despite some variation in luminescence as a result of the growth phase or the particular assay conditions, enumeration by luminescence was found to be a quick, reliable, and highly sensitive method for the
in vitro
detection of leptospires that has the potential to replace more time-consuming methods of enumeration.
Identification and Characterization of the 480-Kilodalton Template-Specific RNA-Dependent RNA Polymerase Complex of
Red Clover Necrotic Mosaic Virus
Authors: Mine Akira , Takeda Atsushi , Taniguchi Takako , Taniguchi Hisaaki , Kaido Masanori , Mise Kazuyuki , Okuno Tetsuro 
Published: April 2010

ABSTRACT

Replication of positive-strand RNA viruses occurs through the assembly of membrane-associated viral RNA replication complexes that include viral replicase proteins, viral RNA templates, and host proteins.
Red clover necrotic mosaic virus
(RCNMV) is a positive-strand RNA plant virus with a genome consisting of RNA1 and RNA2. The two proteins encoded by RNA1, a 27-kDa protein (p27) and an 88-kDa protein containing an RNA-dependent RNA polymerase (RdRP) motif (p88), are essential for RCNMV RNA replication. To analyze RCNMV RNA replication complexes, we used blue-native polyacrylamide gel electrophoresis (BN/PAGE), which enabled us to analyze detergent-solubilized large membrane protein complexes. p27 and p88 formed a complex of 480 kDa in RCNMV-infected plants. As a result of sucrose gradient sedimentation, the 480-kDa complex cofractionated with both endogenous template-bound and exogenous template-dependent RdRP activities. The amount of the 480-kDa complex corresponded to the activity of exogenous template-dependent RdRP, which produced RNA fragments by specifically recognizing the 3′-terminal core promoter sequences of RCNMV RNAs, but did not correspond to the activity of endogenous template-bound RdRP, which produced genome-sized RNAs without the addition of RNA templates. These results suggest that the 480-kDa complex contributes to template-dependent RdRP activities. We subjected those RdRP complexes to affinity purification and analyzed their components using two-dimensional BN/sodium dodecyl sulfate-PAGE (BN/SDS-PAGE) and mass spectrometry. The 480-kDa complex contained p27, p88, and possible host proteins, and the original affinity-purified RdRP preparation contained HSP70, HSP90, and several ribosomal proteins that were not detected in the 480-kDa complex. A model for the formation of RCNMV RNA replication complexes is proposed.
Nonpathogenic Simian Immunodeficiency Virus Infection of Sooty Mangabeys Is Not Associated with High Levels of Autologous Neutralizing Antibodies
Authors: Li Bing , Stefano-Cole Kelly , Kuhrt David M. , Gordon Shari N. , Else James G. , Mulenga Joseph , Allen Susan , Sodora Donald L. , Silvestri Guido , Derdeyn Cynthia A. 
Published: April 2010

ABSTRACT

Simian immunodeficiency virus (SIV) infection of natural-host species, such as sooty mangabeys (SMs), is characterized by a high level of viral replication and a low level of generalized immune activation, despite evidence of an adaptive immune response. Here the ability of SIV-infected SMs to mount neutralizing antibodies (Nab) against autologous virus was compared to that of human immunodeficiency virus type 1 (HIV-1) subtype C-infected subjects. While high levels of Nab were observed in HIV-1 infection, samples obtained at comparable time points from SM exhibited relatively low titers of autologous Nab. Nevertheless, SM plasma with higher Nab titers also contained elevated peripheral CD4
+
T-cell levels, suggesting a potential immunologic benefit for SMs. These data indicate that AIDS resistance in these primates is not due to high Nab titers and raise the possibility that low levels of Nab might be an inherent feature of natural-host SIV infections.
The Crystal Structure of D212 from
Sulfolobus
Spindle-Shaped Virus Ragged Hills Reveals a New Member of the PD-(D/E)XK Nuclease Superfamily
Authors: Menon Smita K. , Eilers Brian J. , Young Mark J. , Lawrence C. Martin 
Published: April 2010

ABSTRACT

Structural studies have made significant contributions to our understanding of
Sulfolobus
spindle-shaped viruses (
Fuselloviridae
), an important model system for archaeal viruses. Continuing these efforts, we report the structure of D212 from
Sulfolobus
spindle-shaped virus Ragged Hills. The overall fold and conservation of active site residues place D212 in the PD-(D/E)XK nuclease superfamily. The greatest structural similarity is found to the archaeal Holliday junction cleavage enzymes, strongly suggesting a role in DNA replication, repair, or recombination. Other roles associated with nuclease activity are also considered.
Through Its Nonstructural Protein NS1, Parvovirus H-1 Induces Apoptosis via Accumulation of Reactive Oxygen Species
Authors: Hristov Georgi , Krämer Melanie , Li Junwei , El-Andaloussi Nazim , Mora Rodrigo , Daeffler Laurent , Zentgraf Hanswalter , Rommelaere Jean , Marchini Antonio 
Published: April 2010

ABSTRACT

The rat parvovirus H-1 (H-1PV) attracts high attention as an anticancer agent, because it is not pathogenic for humans and has oncotropic and oncosuppressive properties. The viral nonstructural NS1 protein is thought to mediate H-1PV cytotoxicity, but its exact contribution to this process remains undefined. In this study, we analyzed the effects of the H-1PV NS1 protein on human cell proliferation and cell viability. We show that NS1 expression is sufficient to induce the accumulation of cells in G
2
phase, apoptosis via caspase 9 and 3 activation, and cell lysis. Similarly, cells infected with wild-type H-1PV arrest in G
2
phase and undergo apoptosis. Furthermore, we also show that both expression of NS1 and H-1PV infection lead to higher levels of intracellular reactive oxygen species (ROS), associated with DNA double-strand breaks. Antioxidant treatment reduces ROS levels and strongly decreases NS1- and virus-induced DNA damage, cell cycle arrest, and apoptosis, indicating that NS1-induced ROS are important mediators of H-1PV cytotoxicity.
Long-Term Evolution of theLuteoviridae: Time Scale and Mode of Virus Speciation
Authors: Pagán Israel , Holmes Edward C. 
Published: April 2010

ABSTRACTDespite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in theLuteoviridaefamily of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulatingLuteoviridaespecies occurred within the last 4 millennia, with intraspecific genetic diversity arising within the last few hundred years. Speciation within theLuteoviridaemay therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature.
Bacteriophage Lambda: a Paradigm Revisited
Authors: Fogg Paul C. M. , Allison Heather E. , Saunders Jon R. , McCarthy Alan J. 
Published: April 2010

ABSTRACT

Bacteriophage lambda has an archetypal immunity system, which prevents the superinfection of its
Escherichia coli
lysogens. It is now known that superinfection can occur with toxigenic lambda-like phages at a high frequency, and here we demonstrate that the superinfection of a lambda lysogen can lead to the acquisition of additional lambda genomes, which was confirmed by Southern hybridization and quantitative PCR. As many as eight integration events were observed but at a very low frequency (6.4 × 10
−4
) and always as multiple insertions at the established primary integration site in
E. coli
. Sequence analysis of the complete immunity region demonstrated that these multiply infected lysogens were not immunity mutants. In conclusion, although lambda superinfection immunity can be confounded, it is a rare event.