bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic Engineering of
Corynebacterium glutamicum
for 2-Ketoisovalerate Production
Authors: Krause Felix S. , Blombach Bastian , Eikmanns Bernhard J. 
Published: October 2010

ABSTRACT

2-Ketoisovalerate is used as a therapeutic agent, and a 2-ketoisovalerate-producing organism may serve as a platform for products deriving from this 2-keto acid. We engineered the wild type of
Corynebacterium glutamicum
for the growth-decoupled production of 2-ketoisovalerate from glucose by deletion of the
aceE
gene encoding the E1p subunit of the pyruvate dehydrogenase complex, deletion of the transaminase B gene
ilvE
, and additional overexpression of the
ilvBNCD
genes, encoding the
l
-valine biosynthetic enzymes acetohydroxyacid synthase (AHAS), acetohydroxyacid isomeroreductase, and dihydroxyacid dehydratase. 2-Ketoisovalerate production was further improved by deletion of the pyruvate:quinone oxidoreductase gene
pqo
. In fed-batch fermentations at high cell densities, the newly constructed strains produced up to 188 ± 28 mM (21.8 ± 3.2 g liter
−1
) 2-ketoisovalerate and showed a product yield of about 0.47 ± 0.05 mol per mol (0.3 ± 0.03 g per g) of glucose and a volumetric productivity of about 4.6 ± 0.6 mM (0.53 ± 0.07 g liter
−1
) 2-ketoisovalerate per h in the overall production phase. In studying the influence of the three branched-chain 2-keto acids 2-ketoisovalerate, 2-ketoisocaproate, and 2-keto-3-methylvalerate on the AHAS activity, we observed a competitive inhibition of the AHAS enzyme by 2-ketoisovalerate.
Variability of
Bartonella
Genotypes among Small Mammals in Spain
Authors: Gil H. , García-Esteban C. , Barandika J. F. , Peig J. , Toledo A. , Escudero R. , Jado I. , Rodríguez-Vargas M. , García-Amil C. , Lobo B. , Roales P. , Rodríguez-Moreno I. , Olmeda A. S. , García-Pérez A. L. , Anda P. 
Published: October 2010

ABSTRACT

In order to study which
Bartonella
genotypes are circulating among small mammals in Spain, we analyzed the spleens of 395 animals from three different areas—247 animals from the Basque Country (northern Spain), 121 animals from Catalonia (northeastern Spain), and 27 animals from Madrid (central Spain)—by a triplex PCR combined with a reverse line blot previously described by our group. The prevalence of
Bartonella
was 26.8% (106/395), and in 4.8% (19/395) of the animals more than one
Bartonella
genotype was detected. The study of
gltA
and the intergenic transcribed spacer in the positive samples demonstrated a large diversity, allowing the assignation of them into 22 genotypes. The most prevalent genotypes were 2 and 3, which are closely related to
Bartonella taylorii
. In addition, nine genotypes were associated with specific mammal species. Genotypes close to the zoonotic
Bartonella grahamii
,
Bartonella elizabethae
, and
Bartonella rochalimae
were also detected. Ten genotypes showed a percentage of similarity with known
Bartonella
species lower than 96%, suggesting the presence of potential new species. Further studies of the impact of these pathogens on human health and especially in cases of febrile illness in Spain are strongly recommended. Furthermore, our method has been updated with 21 new probes in a final panel of 36, which represents a robust molecular tool for clinical and environmental
Bartonella
studies.
Derepression ofINO1Transcription Requires Cooperation between the Ino2p-Ino4p Heterodimer and Cbf1p and Recruitment of the ISW2 Chromatin-Remodeling Complex
Authors: Shetty Ameet , Lopes John M. 
Published: October 2010

ABSTRACTTheSaccharomyces cerevisiaeINO1gene encodes the structural enzyme inositol-3-phosphate synthase for the synthesisde novoof inositol and inositol-containing phospholipids. The transcription ofINO1is completely derepressed in the absence of inositol and choline (I−C−). Derepression requires the binding of the Ino2p-Ino4p basic helix-loop-helix (bHLH) heterodimer to the UASINOpromoter element. We report here the requirement of a third bHLH protein, centromere-binding factor 1 (Cbf1p), for the complete derepression ofINO1transcription. We found that Cbf1p regulatesINO1transcription by binding to sites distal to theINO1promoter and encompassing the upstreamSNA3open reading frame (ORF) and promoter. The binding of Cbf1p requires Ino2p-Ino4p binding to the UASINOsites in theINO1promoter and vice versa, suggesting a cooperative mechanism. Furthermore, Cbf1p binding to the upstream sites was required for the binding of the ISW2 chromatin-remodeling complex to the Ino2p-Ino4p-binding sites on theINO1promoter. Consistent with this, ISW2 was also required for the complete derepression ofINO1transcription.
Suppressor Mutagenesis Identifies a Velvet Complex Remediator of Aspergillus nidulans Secondary Metabolism
Authors: Shaaban Mona I. , Bok Jin Woo , Lauer Carrie , Keller Nancy P. 
Published: October 2010

ABSTRACTFungal secondary metabolites (SM) are bioactive compounds that are important in fungal ecology and, moreover, both harmful and useful in human endeavors (e.g., as toxins and pharmaceuticals). Recently a nuclear heterocomplex termed the Velvet complex, characterized in the model ascomyceteAspergillus nidulans, was found to be critical for SM production. Deletion of two members of the Velvet complex,laeAandveA, results in near loss of SM and defective sexual spore production inA. nidulansand other species. Using a multicopy-suppressor genetics approach, we have isolated anAspergillus nidulansgene namedrsmA(remediation of secondary metabolism) based upon its ability to remediate secondary metabolism in ΔlaeAand ΔveAbackgrounds. Overexpression ofrsmA(OE::rsmA) restores production of sterigmatocystin (ST) (a carcinogenic SM) via transcriptional activation of ST biosynthetic genes. However, defects in sexual reproduction in either ΔlaeAor ΔveAstrains cannot be overcome by OE::rsmA. An intact Velvet complex coupled with an OE::rsmAallele increases SM many fold over the wild-type level, but loss ofrsmAdoes not decrease SM. RsmA encodes a putative bZIP basic leucine zipper-type transcription factor.
Stressosomes Formed inBacillus subtilisfrom the RsbR Protein ofListeria monocytogenesAllow σBActivation following Exposure to either Physical or Nutritional Stress
Authors: Martinez Luis , Reeves Adam , Haldenwang William 
Published: October 2010

ABSTRACTThe general stress regulon ofBacillus subtilisis controlled by σB, a transcription factor that is activated by physical or nutritional stress. InB. subtilis, each of these two stresses is communicated to the primary σBregulators by distinct pathways. Physical stress activation of σBinvolves a large-molecular-mass (>106-Da) structure (stressosome) formed by one or more homologous proteins (RsbRA, -B, -C, and -D) onto which the pathway's principal regulators are bound. The RsbR proteins are thought to be potential receptors for stress signaling.Listeria monocytogenesencodes orthologs of σBand its principal regulators; however, unlikeB. subtilis,L. monocytogenesappears to use the stressosome pathway for both physical and nutritional stress activation of σB. In the current work, aB. subtilisstrain that expressedL. monocytogenes rsbR(rsbRLm) in lieu ofB. subtilis rsbR(rsbRBs) was created and was found to display theListeriaphenotype of σBactivation following exposure to either physical or nutritional stress.B. subtilisexpressing either the RsbR paralogrsbRCorrsbRD, but notrsbRAorrsbRB, as the sole source of RsbR also allowed σBinduction following nutritional stress. It is unclear whether the nutritional stress induction seen in these strains is the result of a direct effect of nutritional stress on stressosome activity or a consequence of the background levels of σBactivation in these strains and the effects of diminished ATP on the downstream phosphorylation reaction needed to reinactivate σB.
Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of
Escherichia coli
Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery
Authors: Ferrières Lionel , Hémery Gaëlle , Nham Toan , Guérout Anne-Marie , Mazel Didier , Beloin Christophe , Ghigo Jean-Marc 
Published: October 2010

ABSTRACT

Random transposon mutagenesis is the strategy of choice for associating a phenotype with its unknown genetic determinants. It is generally performed by mobilization of a conditionally replicating vector delivering transposons to recipient cells using broad-host-range RP4 conjugative machinery carried by the donor strain. In the present study, we demonstrate that bacteriophage Mu, which was deliberately introduced during the original construction of the widely used donor strains SM10 λ
pir
and S17-1 λ
pir
, is silently transferred to
Escherichia coli
recipient cells at high frequency, both by
hfr
and by release of Mu particles by the donor strain. Our findings suggest that bacteriophage Mu could have contaminated many random-mutagenesis experiments performed on Mu-sensitive species with these popular donor strains, leading to potential misinterpretation of the transposon mutant phenotype and therefore perturbing analysis of mutant screens. To circumvent this problem, we precisely mapped Mu insertions in SM10 λ
pir
and S17-1 λ
pir
and constructed a new Mu-free donor strain, MFD
pir
, harboring stable
hfr-
deficient RP4 conjugative functions and sustaining replication of Π-dependent suicide vectors. This strain can therefore be used with most of the available transposon-delivering plasmids and should enable more efficient and easy-to-analyze mutant hunts in
E. coli
and other Mu-sensitive RP4 host bacteria.
Crl Binds to Domain 2 of σ
S
and Confers a Competitive Advantage on a Natural
rpoS
Mutant of
Salmonella enterica
Serovar Typhi
Authors: Monteil Véronique , Kolb Annie , Mayer Claudine , Hoos Sylviane , England Patrick , Norel Françoise 
Published: October 2010

ABSTRACT

The RpoS sigma factor (σ
S
) is the master regulator of the bacterial response to a variety of stresses. Mutants in
rpoS
arise in bacterial populations in the absence of stress, probably as a consequence of a subtle balance between self-preservation and nutritional competence. We characterized here one natural
rpoS
mutant of
Salmonella enterica
serovar Typhi (Ty19). We show that the
rpoS
allele of Ty19 (
rpoS
Ty19
) led to the synthesis of a σ
S
Ty19
protein carrying a single glycine-to-valine substitution at position 282 in σ
S
domain 4, which was much more dependent than the wild-type σ
S
protein on activation by Crl, a chaperone-like protein that increases the affinity of σ
S
for the RNA polymerase core enzyme (E). We used the bacterial adenylate cyclase two-hybrid system to demonstrate that Crl bound to residues 72 to 167 of σ
S
domain 2 and that G282V substitution did not directly affect Crl binding. However, this substitution drastically reduced the ability of σ
S
Ty19
to bind E in a surface plasmon resonance assay, a defect partially rescued by Crl. The modeled structure of the Eσ
S
holoenzyme suggested that substitution G282V could directly disrupt a favorable interaction between σ
S
and E. The
rpoS
Ty19
allele conferred a competitive fitness when the bacterial population was wild type for
crl
but was outcompeted in Δ
crl
populations. Thus, these results indicate that the competitive advantage of the
rpoS
Ty19
mutant is dependent on Crl and suggest that
crl
plays a role in the appearance of
rpoS
mutants in bacterial populations.
GlpR Represses Fructose and Glucose Metabolic Enzymes at the Level of Transcription in the HaloarchaeonHaloferax volcanii
Authors: Rawls Katherine S. , Yacovone Shalane K. , Maupin-Furlow Julie A. 
Published: October 2010

ABSTRACTIn this study, a DeoR/GlpR-type transcription factor was investigated for its potential role as a global regulator of sugar metabolism in haloarchaea, usingHaloferax volcaniias a model organism. Common to a number of haloarchaea and Gram-positive bacterial species, the encodingglpRgene was chromosomally linked with genes of sugar metabolism. InH. volcanii,glpRwas cotranscribed with the downstream phosphofructokinase (PFK;pfkB) gene, and the transcript levels of thisglpR-pfkBoperon were 10- to 20-fold higher when cells were grown on fructose or glucose than when they were grown on glycerol alone. GlpR was required for repression on glycerol based on significant increases in the levels of PFK (pfkB) transcript and enzyme activity detected upon deletion ofglpRfrom the genome. Deletion ofglpRalso resulted in significant increases in both the activity and the transcript (kdgK1) levels of 2-keto-3-deoxy-d-gluconate kinase (KDGK), a key enzyme of haloarchaeal glucose metabolism, when cells were grown on glycerol, compared to the levels obtained for media with glucose. Promoter fusions to a β-galactosidasebgaHreporter revealed that transcription ofglpR-pfkBandkdgK1was modulated by carbon source and GlpR, consistent with quantitative reverse transcription-PCR (qRT-PCR) and enzyme activity assays. The results presented here provide genetic and biochemical evidence that GlpR controls both fructose and glucose metabolic enzymes through transcriptional repression of theglpR-pfkBoperon andkdgK1during growth on glycerol.
Regulation of CodY Activity through Modulation of Intracellular Branched-Chain Amino Acid Pools
Authors: Brinsmade Shaun R. , Kleijn Roelco J. , Sauer Uwe , Sonenshein Abraham L. 
Published: October 2010

ABSTRACTIn several Gram-positive bacterial species, the global transcriptional regulatory protein CodY adjusts the expression of many metabolic genes, apparently in response to changes in the pools of specific metabolites, i.e., the branched-chain amino acids (BCAAs) isoleucine, leucine, and valine (ILV) and the nucleoside triphosphate GTP. CodY not only responds to these metabolites as measuredin vitrobut also regulates the genes that direct their synthesis. We have constructed a set of strains lacking binding sites for the CodY protein incisat loci coding for the ILV biosynthetic machinery, effectively overexpressing these genes in an attempt to modulate the ILV input signal to CodY. Metabolite analyses of strains derepressed for genes needed for ILV synthesis revealed more than a 6-fold increase in the valine pool and a 2-fold increase in the isoleucine and leucine pools. Accumulation of the branched-chain amino acids was accompanied by a 24-fold induction of thebkdoperon (required for branched-chain fatty acid synthesis) and 6-fold hyperrepression of the CodY-regulatedyhdGandyufNgenes, demonstrating that CodY perceives intracellular fluctuations in at least one if its input signals. We conclude that changes in the rate of endogenous ILV synthesis serve as an important signal for CodY-mediated gene regulation.
Evolution and Population Structure of
Salmonella enterica
Serovar Newport
Authors: Sangal Vartul , Harbottle Heather , Mazzoni Camila J. , Helmuth Reiner , Guerra Beatriz , Didelot Xavier , Paglietti Bianca , Rabsch Wolfgang , Brisse Sylvain , Weill François-Xavier , Roumagnac Philippe , Achtman Mark 
Published: October 2010

ABSTRACT

Salmonellosis caused by
Salmonella enterica
serovar Newport is a major global public health concern, particularly because
S.
Newport isolates that are resistant to multiple drugs (MDR), including third-generation cephalosporins (MDR-AmpC phenotype), have been commonly isolated from food animals. We analyzed 384
S.
Newport isolates from various sources by a multilocus sequence typing (MLST) scheme to study the evolution and population structure of the serovar. These were compared to the population structure of
S. enterica
serovars Enteritidis, Kentucky, Paratyphi B, and Typhimurium. Our
S.
Newport collection fell into three lineages, Newport-I, Newport-II, and Newport-III, each of which contained multiple sequence types (STs). Newport-I has only a few STs, unlike Newport-II or Newport-III, and has possibly emerged recently. Newport-I is more prevalent among humans in Europe than in North America, whereas Newport-II is preferentially associated with animals. Two STs of Newport-II encompassed all MDR-AmpC isolates, suggesting recent global spread after the acquisition of the
bla
CMY-2
gene. In contrast, most Newport-III isolates were from humans in North America and were pansusceptible to antibiotics. Newport was intermediate in population structure to the other serovars, which varied from a single monophyletic lineage in
S.
Enteritidis or
S.
Typhimurium to four discrete lineages within
S.
Paratyphi B. Both mutation and homologous recombination are responsible for diversification within each of these lineages, but the relative frequencies differed with the lineage. We conclude that serovars of
S. enterica
provide a variety of different population structures.
Genome Sequence of the Polysaccharide-Degrading, Thermophilic AnaerobeSpirochaeta thermophilaDSM 6192
Authors: Angelov Angel , Liebl Susanne , Ballschmiter Meike , Bömeke Mechthild , Lehmann Rüdiger , Liesegang Heiko , Daniel Rolf , Liebl Wolfgang 
Published: October 2010

ABSTRACTSpirochaeta thermophilais a thermophilic, free-living anaerobe that is able to degrade various α- and β-linked sugar polymers, including cellulose. We report here the complete genome sequence ofS. thermophilaDSM 6192, which is the first genome sequence of a thermophilic, free-living member of theSpirochaetesphylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.
Whole-Genome Sequences of Thirteen Isolates of
Borrelia burgdorferi
Authors: Schutzer Steven E. , Fraser-Liggett Claire M. , Casjens Sherwood R. , Qiu Wei-Gang , Dunn John J. , Mongodin Emmanuel F. , Luft Benjamin J. 
Published: October 2010

ABSTRACT

Borrelia burgdorferi
is a causative agent of Lyme disease in North America and Eurasia. The first complete genome sequence of
B. burgdorferi
strain 31, available for more than a decade, has assisted research on the pathogenesis of Lyme disease. Because a single genome sequence is not sufficient to understand the relationship between genotypic and geographic variation and disease phenotype, we determined the whole-genome sequences of 13 additional
B. burgdorferi
isolates that span the range of natural variation. These sequences should allow improved understanding of pathogenesis and provide a foundation for novel detection, diagnosis, and prevention strategies.
Emergence of
Pseudomonas aeruginosa
Strains Producing High Levels of Persister Cells in Patients with Cystic Fibrosis
Authors: Mulcahy Lawrence R. , Burns Jane L. , Lory Stephen , Lewis Kim 
Published: October 2010

ABSTRACT

The majority of cystic fibrosis (CF) patients succumb to a chronic infection of the airway with
Pseudomonas aeruginosa
. Paradoxically, pathogenic strains are often susceptible to antibiotics, but the infection cannot be eradicated with antimicrobial therapy. We find that in a majority of patients with airway infections, late isolates of
P. aeruginosa
produce increased levels of drug-tolerant persister cells. The genomes of a clonal pair of early/late isolates from a single patient have been previously sequenced, and the late isolate (obtained at age 96 months) showed a 100-fold increase in persister levels. The 96-month isolate carries a large number of mutations, including a mutation in
mutS
that confers a hypermutator phenotype. There is also a mutation in the
mexZ
repressor controlling the expression of the MexXY-OprM multidrug pump, which results in a moderate increase in the ofloxacin, carbenicillin, and tobramycin MICs. Knocking out the
mexXY
locus restored the resistance to that of the parent strain but did not affect the high levels of persisters formed by the 96-month isolate. This suggests that the late isolate is a high-persister (
hip
) mutant. Increased persister formation was observed in exponential phase, stationary phase, and biofilm populations of the 96-month isolate. Analysis of late isolates from 14 additional patients indicated that 10 of them are
hip
mutants. Most of these
hip
mutants did not have higher drug resistance. Increased persister formation appears to be their sole mechanism for surviving chemotherapy. Taken together, these findings suggest a link between persisters and recalcitrance of CF infection and identify an overlooked culprit—high-persister mutants producing elevated levels of drug-tolerant cells. Persisters may play a similarly critical role in the recalcitrance of other chronic infections.
A prospective evaluation of air quality and workers' health in broiler and layer operations
Authors: Senthilselvan Ambikaipakan , Beach Jeremy , Feddes John , Cherry Nicola , Wenger Irene 
Published: October 2010

ObjectivesIn developed countries, poultry are raised in totally confined buildings in which workers are exposed to indoor airborne contaminants. A prospective study was conducted to investigate the relationship between workers' respiratory health and airborne contaminants during the life cycle of broiler and layer flocks.MethodsSeventeen layer and 16 broiler operations were chosen within a 200 km radius of Edmonton. An attempt was made to visit each broiler operation twice during the winter and summer seasons in the early and later periods of the 6-week production cycle and visit each layer operation three times during the early, middle and later periods of the 40-week production cycle.ResultsIn broiler operations, respirable particle counts, total dust and endotoxin concentrations, and ammonia levels increased with flock age, while mean endotoxin load (EU/mg) decreased in the winter and summer seasons. Increases in dust and endotoxin concentrations in the winter season were not statistically significance. Mean endotoxin concentration increased and mean dust concentration and ammonia level decreased with flock age in layer operations, although not all these changes were statistically significant. Mean across-shift decrements in FEV1and FVC increased with flock age among workers from layer operations. Endotoxin concentration was significantly associated with across-shift changes in FEV1among workers in layer operations.ConclusionIn our study, changes in lung function appear more closely associated with changes in endotoxin than other contaminants. Changes in indoor environmental conditions occurring in poultry barns which are dependent on the flock age may affect workers' health in poultry operations.
The risk of hospitalisation for infectious pneumonia in mineral dust exposed industries: Table 1
Authors: Koh Dong-Hee , Moon Ki-Tae , Kim Jeong-Youn , Choe Seong-Weon 
Published: October 2010

ObjectivesThe purpose of the study was to elucidate the relationship between industries characterised by mineral dust exposure and infectious pneumonia.MethodsThe authors applied a retrospective record linkage design and used the nationwide specific health examination database and identified industries where mineral dust exposure occurs and a control group composed of workers who had been exposed to noise-only during a 2000–2004 period. The database was matched with National Health Insurance claim records to identify pneumonia admissions from 2000 to 2005. The indirectly standardised admission ratios (SARs) for pneumonia admissions were estimated by comparing mineral dust exposed industry workers with noise-only exposed workers.ResultsThe authors found significantly elevated SARs in both men (1.54, 95% CI 1.13 to 2.05) and women (3.23, 95% CI 1.40 to 6.37) working in the cement, lime, plaster and plaster products industries, and only in men working in the cast-metals industry (foundry) (1.64, 95% CI 1.25 to 2.11).ConclusionsThese results support the association between mineral dust exposure, as well as metal fumes, and infectious pneumonia.