bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preferential Brain Homing following Intranasal Administration ofTrypanosoma cruzi
Authors: Caradonna Kacey , PereiraPerrin Mercio 
Published: January 2009

ABSTRACTThe Chagas’ disease parasiteTrypanosoma cruzicommonly infects humans through skin abrasions or mucosa from reduviid bug excreta. Yet most studies on animal models start with subcutaneous or intraperitoneal injections, a distant approximation of the skin abrasion route. We show here that atraumatic placement ofT. cruziin the mouse nasal cavity produced low parasitemia, high survival rates, and preferential brain invasion compared to the case with subcutaneously injected parasites. Brain invasion was particularly prominent in the basal ganglia, peaked at a time when parasitemia was no longer detectable, and elicited a relatively large number of inflammatory foci. Yet, based on motor behavioral parameters and staining with Fluoro-Jade C, a dye that specifically recognizes apoptotic and necrotic neurons, brain invasion did not cause neurodegenerative events, in contrast to the neurodegeneration in the enteric nervous system. The results indicate that placement ofT. cruzion the mucosa in the mouse nasal cavity establishes a systemic infection with a robust yet harmless infection of the brain, seemingly analogous to disease progression in humans. The model may facilitate studies designed to understand mechanisms underlyingT. cruziinfection of the central nervous system.
Vaccination Route That Induces Transforming Growth Factor β Production Fails To Elicit Protective Immunity againstLeishmania donovaniInfection
Authors: Bhowmick Sudipta , Mazumdar Tuhina , Ali Nahid 
Published: January 2009

ABSTRACTBALB/c mice immunized intraperitoneally (i.p.) and intravenously (i.v.) withLeishmania donovanipromastigote membrane antigens (LAg), either free or encapsulated in liposomes, were protected against challenge infection withL. donovani, whereas mice immunized by the subcutaneous (s.c.) and intramuscular routes were not protected. Protected mice showed strong parasite resistance in both the liver and spleen, along with enhanced immunoglobulin G2a and delayed-type hypersensitivity responses. Again, mice vaccinated through the i.p. and i.v. routes showed high levels of NO production after challenge infection. s.c. vaccination resulted in an increased capacity of the spleen cells to produce prechallenge transforming growth factor β (TGF-β) levels during the in vitro antigen recall response, whereas i.p. immunization induced production of prechallenge gamma interferon, interleukin-12 (IL-12), and IL-4 levels, with a Th1 bias. Exposure to antigen-stimulated splenocyte supernatants of i.p. but not s.c. immunized mice activated macrophages for in vitro parasite killing. As an enhanced level of TGF-β was detected in supernatants from unprotected s.c. immunized mice, neutralization by anti-TGF-β antibody enhanced in vitro macrophage killing activity. The suppressive role of this cytokine was evaluated in vivo by vaccination with liposomal LAg and anti-TGF-β antibody. Upon parasite challenge, these animals showed significant protection in both the liver and spleen. Moreover, the addition of recombinant TGF-β in splenocyte supernatants of i.p. immunized mice in vitro as well as in vivo inhibited the protective ability of the macrophages by the i.p. route. Thus, the induction of high prechallenge TGF-β limits the efficacy of vaccination by routes that are nonprotective.
Complete Genome Sequence ofErythrobacter litoralisHTCC2594
Authors: Oh Hyun-Myung , Giovannoni Stephen J. , Ferriera Steve , Johnson Justin , Cho Jang-Cheon 
Published: January 2009

ABSTRACTErythrobacter litoralishas been known as a bacteriochlorophylla-containing, aerobic, anoxygenic, phototrophic bacterium. Here we announce the complete genome sequence ofE. litoralisHTCC2594, which is devoid of phototrophic potential.E. litoralisHTCC2594, isolated by dilution-to-extinction culturing from seawater, could not carry out aerobic anoxygenic phototrophy and lacked genes for bacteriochlorophyllabiosynthesis and photosynthetic reaction center proteins.
Genetic Analysis of the Invariant Residue G791 in
Escherichia coli
16S rRNA Implicates RelA in Ribosome Function
Authors: Kim Hong-Man , Ryou Sang-Mi , Song Woo-Seok , Sim Se-Hoon , Cha Chang-Jun , Han Seung Hyun , Ha Nam-Chul , Kim Jae-Hong , Bae Jeehyeon , Cunningham Philip R. , Lee Kangseok 
Published: January 2009

ABSTRACT

Previous studies identified G791 in
Escherichia coli
16S rRNA as an invariant residue for ribosome function. In order to establish the functional role of this residue in protein synthesis, we searched for multicopy suppressors of the mutant ribosomes that bear a G-to-U substitution at position 791. We identified
relA
, a gene whose product has been known to interact with ribosomes and trigger a stringent response. Overexpression of RelA resulted in the synthesis of approximately 1.5 times more chloramphenicol acetyltransferase (CAT) protein than could be synthesized by the mutant ribosomes in the absence of RelA overexpression. The ratio of mutant rRNA to the total ribosome pool was not changed, and the steady-state level of CAT mRNA was decreased by RelA overexpression. These data confirmed that the phenotype of RelA as a multicopy suppressor of the mutant ribosome did not result from the enhanced synthesis of mutant rRNA or CAT mRNA from the plasmid. To test whether the phenotype of RelA was related to the stringent response induced by the increased cellular level of (p)ppGpp, we screened for mutant RelA proteins whose overexpression enhances CAT protein synthesis by the mutant ribosomes as effectively as wild-type RelA overexpression and then screened for those whose overexpression does not produce sufficiently high levels of (p)ppGpp to trigger the stringent response under the condition of amino acid starvation. Overexpression of the isolated mutant RelA proteins resulted in the accumulation of (p)ppGpp in cells, which was amounted to approximately 18.2 to 38.9% of the level of (p)ppGpp found in cells that overexpress the wild-type RelA. These findings suggest that the function of RelA as a multicopy suppressor of the mutant ribosome does not result from its (p)ppGpp synthetic activity. We conclude that RelA has a previously unrecognized role in ribosome function.
Mutational Analysis and Homology-Based Modeling of the IntDOT Core-Binding Domain
Authors: Malanowska Karolina , Cioni Joel , Swalla Brian M. , Salyers Abigail , Gardner Jeffrey F. 
Published: January 2009

ABSTRACT
Tyrosine recombinases mediate a wide range of important genetic rearrangement reactions. Models for tyrosine recombinases have been based largely on work done on the integrase of phage lambda and recombinases like Cre, Flp, and XerC/D. All of these recombinases share a common amino acid signature that is important for catalysis. Several conjugative transposons (CTns) encode recombinases that are also members of the tyrosine recombinase family, but the reaction that they catalyze differs in that recombination does not require homology in the attachment sites. In this study, we examine the role of the core-binding (CB) domain of the CTnDOT integrase (IntDOT) that is located adjacent to the catalytic domain of the protein. Since there is no crystal structure for any of the CTn integrases, we began with a predicted three-dimensional structure produced by homology-based modeling. Amino acid substitutions were made at positions predicted by the model to be close to the DNA. Mutant proteins were tested for the ability to mediate integration in vivo and for in vitro DNA-binding, cleavage, and ligation activities. We identified for the first time nonconserved amino acid residues in the CB domain that are important for catalytic activity. Mutant proteins with substitutions at three positions in the CB domain are defective for DNA cleavage but still proficient in ligation. The positions of the residues in the complex suggest that the mutant residues affect the positioning of the cleaved phosphodiester bond in the active site without disruption of the ligation step.
Three-Dimensional Macromolecular Organization of CryofixedMyxococcus xanthusBiofilms as Revealed by Electron Microscopic Tomography
Authors: Palsdottir Hildur , Remis Jonathan P. , Schaudinn Christoph , O'Toole Eileen , Lux Renate , Shi Wenyuan , McDonald Kent L. , Costerton J. William , Auer Manfred 
Published: January 2009

ABSTRACTDespite the fact that most bacteria grow in biofilms in natural and pathogenic ecosystems, very little is known about the ultrastructure of their component cells or about the details of their community architecture. We used high-pressure freezing and freeze-substitution to minimize the artifacts of chemical fixation, sample aggregation, and sample extraction. As a further innovation we have, for the first time in biofilm research, used electron tomography and three-dimensional (3D) visualization to better resolve the macromolecular 3D ultrastructure of a biofilm. This combination of superb specimen preparation and greatly improved resolution in thezaxis has opened a window in studies ofMyxococcus xanthuscell ultrastructure and biofilm community architecture. New structural information on the chromatin body, cytoplasmic organization, membrane apposition between adjacent cells, and structure and distribution of pili and vesicles in the biofilm matrix is presented.
The
Thermotoga maritima
Trk Potassium Transporter—from Frameshift to Function
Authors: Johnson Hope A. , Hampton Eric , Lesley Scott A. 
Published: January 2009

ABSTRACT

The gene for the
Thermotoga maritima
Trk potassium transporter component TrkA was originally thought to be a frameshift mutation and not to encode a functional protein. However, expression from this gene yielded a complex consisting of two distinct proteins designated TM1088A and -B. Genetic complementation of
Escherichia coli
mutants unable to transport potassium suggests that TM1088A/B is part of a functional Trk potassium transporter complex with the membrane protein TM1089. The protein structure for TM1088A shows a characteristic Rossmann fold indicating an NAD
+
binding site and has structural similarity to potassium channel-related proteins. Ligand binding studies indicated that ATP, ADP, and AMP stabilized TM1088A to a much greater degree than NADH and NAD, consistent with the crystal structure of TM1088A, which contains a bound AMP natural ligand at the characteristic GXGXXG nucleotide binding site. Mutation of single and all glycines at this nucleotide binding site eliminated in vitro protein stabilization by the ligand, yet these mutated proteins could still functionally complement the
E. coli
potassium uptake mutants. We predict that this new two-subunit class of TrkA proteins is present in a number of organisms. A further subclass of the predicted two-subunit TrkA proteins lack an identifiable membrane-spanning subunit of the Trk K
+
transporter. This class, as exemplified by
Mycobacterium tuberculosis
, did not complement
E. coli
potassium transport with the native
E. coli
TrkH; thus, it may require a novel TrkH-like protein for activity or provide an alternate function in vivo.
Psychrobacter arcticus
273-4 Uses Resource Efficiency and Molecular Motion Adaptations for Subzero Temperature Growth
Authors: Bergholz Peter W. , Bakermans Corien , Tiedje James M. 
Published: January 2009

ABSTRACT

Permafrost soils are extreme environments that exert low-temperature, desiccation, and starvation stress on bacteria over thousands to millions of years. To understand how
Psychrobacter arcticus
273-4 survived for >20,000 years in permafrost, transcriptome analysis was performed during growth at 22°C, 17°C, 0°C, and −6°C using a mixed-effects analysis of variance model. Genes for transcription, translation, energy production, and most biosynthetic pathways were downregulated at low temperatures. Evidence of isozyme exchange was detected over temperature for
d
-alanyl-
d
-alanine carboxypeptidases (
dac1
and
dac2
), DEAD-box RNA helicases (
csdA
and Psyc_0943), and energy-efficient substrate incorporation pathways for ammonium and acetate. Specific functions were compensated by upregulation of genes at low temperature, including genes for the biosynthesis of proline, tryptophan, and methionine. RNases and peptidases were generally upregulated at low temperatures. Changes in energy metabolism, amino acid metabolism, and RNase gene expression were consistent with induction of a resource efficiency response. In contrast to results observed for other psychrophiles and mesophiles, only
clpB
and
hsp33
were upregulated at low temperature, and there was no upregulation of other chaperones and peptidyl-prolyl isomerases.
relA
,
csdA
, and
dac2
knockout mutants grew more slowly at low temperature, but a
dac1
mutant grew more slowly at 17°C. The combined data suggest that the basal biological machinery, including translation, transcription, and energy metabolism, is well adapted to function across the growth range of
P. arcticus
from −6°C to 22°C, and temperature compensation by gene expression was employed to address specific challenges to low-temperature growth.
Roles of
Agrobacterium tumefaciens
RirA in Iron Regulation, Oxidative Stress Response, and Virulence
Authors: Ngok-Ngam Patchara , Ruangkiattikul Nantaporn , Mahavihakanont Aekkapol , Virgem Susan S. , Sukchawalit Rojana , Mongkolsuk Skorn 
Published: January 2009

ABSTRACT

The analysis of genetics and physiological functions of
Agrobacterium tumefaciens
RirA (rhizobial iron regulator) has shown that it is a transcription regulator and a repressor of iron uptake systems. The
rirA
mutant strain (NTLrirA) overproduced siderophores and exhibited a highly constitutive expression of genes involved in iron uptake (
fhuA
,
irp6A
, and
fbpA
) compared to that of the wild-type strain (NTL4). The deregulation in the iron control of iron uptake in NTLrirA led to iron overload in the cell, which was supported by the observation that the NTLrirA mutant was more sensitive than wild-type NTL4 to an iron-activated antibiotic, streptonigrin. The NTLrirA mutant was more sensitive than the parental strain to oxidants, including hydrogen peroxide, organic hydroperoxide, and a superoxide generator, menadione. However, the addition of an iron chelator, 2,2′-dipyridyl, reversed the mutant hypersensitivity to H
2
O
2
and organic hydroperoxide, indicating the role of iron in peroxide toxicity. Meanwhile, the reduced level of superoxide dismutase (SodBIII) was partly responsible for the menadione-sensitive phenotype of the NTLrirA mutant. The NTLrirA mutant showed a defect in tumorigenesis on tobacco leaves, which likely resulted from the increased sensitivity of NTLrirA to oxidants and the decreased ability of NTLrirA to induce virulence genes (
virB
and
virE
). These data demonstrated that RirA is important for
A. tumefaciens
during plant-pathogen interactions.
Pneumolysin Localizes to the Cell Wall of
Streptococcus pneumoniae
Authors: Price Katherine E. , Camilli Andrew 
Published: January 2009

ABSTRACT

Streptococcus pneumoniae
is the causative agent of multiple diseases, including otitis media, pneumonia, bacteremia, and meningitis. Pneumolysin (Ply), a member of the cholesterol-dependent cytolytic pore-forming toxins, is produced by virtually all clinical isolates of
S. pneumoniae
, and strains in which the Ply gene has been deleted are severely attenuated in mouse models of infection. In contrast to all other members of the cholesterol-dependent cytolysin family, Ply lacks a signal peptide for export. Instead, Ply has been hypothesized to be released upon autolysis or, alternatively, via a nonautolytic mechanism that remains ill defined. We determined by use of cell fractionation and Western blotting that, during in vitro growth, exported Ply is localized primarily to the cell wall compartment in 18 different serotypes in the absence of detectable cell lysis. Hemolytic assays revealed that this cell wall-localized Ply is active. Additionally, cell wall-localized Ply is accessible to extracellular protease and is detergent releasable.
The
Pseudomonas aeruginosa
Sensor Kinase KinB Negatively Controls Alginate Production through AlgW-Dependent MucA Proteolysis
Authors: Damron F. Heath , Qiu Dongru , Yu Hongwei D. 
Published: January 2009

ABSTRACT

Mucoidy, or overproduction of the exopolysaccharide known as alginate, in
Pseudomonas aeruginosa
is a poor prognosticator for lung infections in cystic fibrosis. Mutation of the anti-σ factor MucA is a well-accepted mechanism for mucoid conversion. However, certain clinical mucoid strains of
P. aeruginosa
have a wild-type (wt)
mucA
. Here, we describe a loss-of-function mutation in
kinB
that causes overproduction of alginate in the wt
mucA
strain PAO1. KinB is the cognate histidine kinase for the transcriptional activator AlgB. Increased alginate production due to inactivation of
kinB
was correlated with high expression at the alginate-related promoters P

algU

and P

algD

. Deletion of alternative σ factor RpoN (σ
54
) or the response regulator AlgB in
kinB
mutants decreased alginate production to wt nonmucoid levels. Mucoidy was restored in the
kinB algB
double mutant by expression of wt AlgB or phosphorylation-defective AlgB.D59N, indicating that phosphorylation of AlgB was not required for alginate overproduction when
kinB
was inactivated. The inactivation of the DegS-like protease AlgW in the
kinB
mutant caused loss of alginate production and an accumulation of the hemagglutinin (HA)-tagged MucA. Furthermore, we observed that the
kinB
mutation increased the rate of HA-MucA degradation. Our results also indicate that AlgW-mediated MucA degradation required
algB
and
rpoN
in the
kinB
mutant. Collectively, these studies indicate that KinB is a negative regulator of alginate production in wt
mucA
strain PAO1.
The Sac10b Homolog in
Methanococcus maripaludis
Binds DNA at Specific Sites
Authors: Liu Yuchen , Guo Li , Guo Rong , Wong Richard L. , Hernandez Hilda , Hu Jinchuan , Chu Yindi , Amster I. Jonathan , Whitman William B. , Huang Li 
Published: January 2009

ABSTRACT

The Sac10b protein family, also known as Alba, is widely distributed in
Archaea
. Sac10b homologs in thermophilic
Sulfolobus
species are very abundant. They bind both DNA and RNA with high affinity and without sequence specificity, and their physiological functions are still not fully understood. Mma10b from the euryarchaeote
Methanococcus maripaludis
is a mesophilic member of the Sac10b family. Mma10b is not abundant and constitutes only ∼0.01% of the total cellular protein. Disruption of mma10b resulted in poor growth of the mutant in minimal medium at near the optimal growth temperature but had no detectable effect on growth in rich medium. Quantitative proteomics, real time reverse transcription-PCR, and enzyme assays revealed that the expression levels of some genes involved in CO
2
assimilation and other activities were changed in the Δmma10b mutant. Chromatin immunoprecipitation suggested a direct association of Mma10b with an 18-bp DNA binding motif in vivo. Electrophoretic mobility shift assays and DNase I footprinting confirmed that Mma10b preferentially binds specific sequences of DNA with an apparent
K

d

in the 100 nM range. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from that of homologs in thermophiles.
Copper Acquisition Is Mediated by YcnJ and Regulated by YcnK and CsoR in
Bacillus subtilis
Authors: Chillappagari Shashi , Miethke Marcus , Trip Hein , Kuipers Oscar P. , Marahiel Mohamed A. 
Published: January 2009

ABSTRACT

Copper is an essential cofactor for many enzymes, and at over a threshold level, it is toxic for all organisms. To understand the mechanisms underlying copper homeostasis of the gram-positive bacterium
Bacillus subtilis
, we have performed microarray studies under copper-limiting conditions. These studies revealed that the
ycnJ
gene encodes a protein that plays an important role in copper metabolism, as it shows a significant, eightfold upregulation under copper-limiting conditions and its disruption causes a growth-defective phenotype under copper deprivation as well as a reduced intracellular content of copper. Native gel shift experiments with the periplasmic N-terminal domain of the YcnJ membrane protein (135 residues) disclosed its strong affinity to Cu(II) ions in vitro. Inspection of the upstream sequence of
ycnJ
revealed that the
ycnK
gene encodes a putative transcriptional regulator, whose deletion caused an elevated expression of
ycnJ
, especially under conditions of copper excess. Further studies demonstrated that the recently identified copper efflux regulator CsoR also is involved in the regulation of
ycnJ
expression, leading to a new model for copper homeostasis in
B. subtilis
.
A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other β-Hemolytic Streptococci
Authors: Davies Mark R. , Shera Josephine , Van Domselaar Gary H. , Sriprakash Kadaba S. , McMillan David J. 
Published: January 2009

ABSTRACTLateral gene transfer is a significant contributor to the ongoing evolution of many bacterial pathogens, including β-hemolytic streptococci. Here we provide the first characterization of a novel integrative conjugative element (ICE), ICESde3396, fromStreptococcus dysgalactiaesubsp.equisimilis(group G streptococcus [GGS]), a bacterium commonly found in the throat and skin of humans. ICESde3396 is 64 kb in size and encodes 66 putative open reading frames. ICESde3396 shares 38 open reading frames with a putative ICE fromStreptococcus agalactiae(group B streptococcus [GBS]), ICESa2603. In addition to genes involves in conjugal processes, ICESde3396 also carries genes predicted to be involved in virulence and resistance to various metals. A major feature of ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb internal recombinogenic region containing four unique gene clusters, which appear to have been acquired from streptococcal and nonstreptococcal bacterial species. The four clusters include two cadmium resistance operons, an arsenic resistance operon, and genes with orthologues in a group A streptococcus (GAS) prophage. Streptococci that naturally harbor ICESde3396 have increased resistance to cadmium and arsenate, indicating the functionality of genes present in the 18-kb recombinogenic region. By marking ICESde3396 with a kanamycin resistance gene, we demonstrate that the ICE is transferable to other GGS isolates as well as GBS and GAS. To investigate the presence of the ICE in clinical streptococcal isolates, we screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the presence of three separate regions of ICESde3396. Eleven isolates possessed all three regions, suggesting they harbored ICESde3396-like elements. Another four isolates possessed ICESa2603-like elements. We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider β-hemolytic streptococcal population.