bluuebunny/crossref_metadata_2025_split huggingface dataset:
BglJ-RcsB Heterodimers Relieve Repression of theEscherichia coli bglOperon by H-NS
Authors: Venkatesh G. Raja , Kembou Koungni Frant Carlot , Paukner Andreas , Stratmann Thomas , Blissenbach Birgit , Schnetz Karin 
Published: October 2010

ABSTRACTRcsB is the response regulator of the complex Rcs two-component system, which senses perturbations in the outer membrane and peptidoglycan layer. BglJ is a transcriptional regulator whose constitutive expression causes activation of the H-NS- and StpA-repressedbgl(aryl-β,d-glucoside) operon inEscherichia coli. RcsB and BglJ both belong to the LuxR-type family of transcriptional regulators with a characteristic C-terminal DNA-binding domain. Here, we show that BglJ and RcsB interact and form heterodimers that presumably bind upstream of thebglpromoter, as suggested by mutation of a sequence motif related to the consensus sequence for RcsA-RcsB heterodimers. Heterodimerization of BglJ-RcsB and relief of H-NS-mediated repression ofbglby BglJ-RcsB are apparently independent of RcsB phosphorylation. In addition, we show that LeuO, a pleiotropic LysR-type transcriptional regulator, likewise binds to thebglupstream regulatory region and relieves repression ofbglindependently of BglJ-RcsB. Thus, LeuO can affectbgldirectly, as shown here, and indirectly by activating the H-NS-repressedyjjQ-bglJoperon, as shown previously. Taken together, heterodimer formation of RcsB and BglJ expands the role of the Rcs two-component system and the network of regulators affecting thebglpromoter.
Genomic Island 2 Is an Unstable Genetic Element Contributing toBrucellaLipopolysaccharide Spontaneous Smooth-to-Rough Dissociation
Authors: Mancilla Marcos , López-Goñi Ignacio , Moriyón Ignacio , Zárraga Ana María 
Published: October 2010

ABSTRACTBrucellais a Gram-negative bacterium that causes a worldwide-distributed zoonosis. The genus includes smooth (S) and rough (R) species that differ in the presence or absence, respectively, of the O-polysaccharide of lipopolysaccharide. In S brucellae, the O-polysaccharide is a critical diagnostic antigen and a virulence determinant. However, S brucellae spontaneously dissociate into R forms, a problem in antigen and S vaccine production. Spontaneous R mutants ofBrucella abortus,Brucella melitensis, andBrucella suiscarried the chromosomal scar corresponding to genomic island 2 (GI-2) excision, an event causing the loss of thewboAandwboBO-polysaccharide genes, and the predicted excised circular intermediate was identified inB. abortus,B. melitensis, andB. suiscultures. Moreover, disruption of a putative phage integrase gene inB. abortusGI-2 caused a reduction in O-polysaccharide loss rates under conditions promoting S-R dissociation. However, spontaneous R mutants not carrying the GI-2 scar were also detected. These results demonstrate that the phage integrase-related GI-2 excision is a cause of S-R brucella dissociation and that other undescribed mechanisms must also be involved. In the RBrucellaspecies, previous works have shown thatBrucella ovisbut notBrucella canislacks GI-2, and a chromosomal scar identical to those in R mutants was observed. These results suggest that the phage integrase-promoted GI-2 excision played a role inB. ovisspeciation and are consistent with other evidence, suggesting that this species andB. canishave emerged as two independent lineages.
Biochemical Characterization of Individual Components of the
Allochromatium vinosum
DsrMKJOP Transmembrane Complex Aids Understanding of Complex Function
In Vivo
Authors: Grein Fabian , Pereira Inês A. C. , Dahl Christiane 
Published: October 2010

ABSTRACT

The DsrMKJOP transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying FeS centers and
b
- and
c
-type cytochromes as cofactors. In this study, the complex was isolated from the purple sulfur bacterium
Allochromatium vinosum
and individual components were characterized as recombinant proteins. The two integral membrane proteins DsrM and DsrP were successfully produced in
Escherichia coli
C43(DE3) and C41(DE3), respectively. DsrM was identified as a diheme cytochrome
b
, and the two hemes were found to be in low-spin state. Their midpoint redox potentials were determined to be +60 and +110 mV. Although no hemes were predicted for DsrP, it was also clearly identified as a
b
-type cytochrome. To the best of our knowledge, this is the first time that heme binding has been experimentally proven for a member of the NrfD protein family. Both cytochromes were partly reduced after addition of a menaquinol analogue, suggesting interaction with quinones
in vivo
. DsrO and DsrK were both experimentally proven to be FeS-containing proteins. In addition, DsrK was shown to be membrane associated, and we propose a monotopic membrane anchoring for this protein. Coelution assays provide support for the proposed interaction of DsrK with the soluble cytoplasmic protein DsrC, which might be its substrate. A model for the function of DsrMKJOP in the purple sulfur bacterium
A. vinosum
is presented.
Expression of the
Streptomyces coelicolor
SoxR Regulon Is Intimately Linked with Actinorhodin Production
Authors: Dela Cruz Rica , Gao Yang , Penumetcha Sahitya , Sheplock Rebecca , Weng Katherine , Chander Monica 
Published: October 2010

ABSTRACT

The [2Fe-2S]-containing transcription factor SoxR is conserved in diverse bacteria. SoxR is traditionally known as the regulator of a global oxidative stress response in
Escherichia coli
, but recent studies suggest that this function may be restricted to enteric bacteria. In the vast majority of nonenterics, SoxR is predicted to mediate a response to endogenously produced redox-active metabolites. We have examined the regulation and function of the SoxR regulon in the model antibiotic-producing filamentous bacterium
Streptomyces coelicolor
. Unlike the
E. coli soxR
deletion mutant, the
S. coelicolor
equivalent is not hypersensitive to oxidants, indicating that SoxR does not potentiate antioxidant defense in the latter. SoxR regulates five genes in
S. coelicolor
, including those encoding a putative ABC transporter, two oxidoreductases, a monooxygenase, and a possible NAD-dependent epimerase/dehydratase. Expression of these genes depends on the production of the benzochromanequinone antibiotic actinorhodin and requires intact [2Fe-2S] clusters in SoxR. These data indicate that actinorhodin, or a redox-active precursor, modulates SoxR activity in
S. coelicolor
to stimulate the production of a membrane transporter and proteins with homology to actinorhodin-tailoring enzymes. While the role of SoxR in
S. coelicolor
remains under investigation, these studies support the notion that SoxR has been adapted to perform distinct physiological functions to serve the needs of organisms that occupy different ecological niches and face different environmental challenges.
DosS Responds to a Reduced Electron Transport System To Induce the
Mycobacterium tuberculosis
DosR Regulon
Authors: Honaker Ryan W. , Dhiman Rakesh K. , Narayanasamy Prabagaran , Crick Dean C. , Voskuil Martin I. 
Published: October 2010

ABSTRACT

The DosR regulon in
Mycobacterium tuberculosis
is involved in respiration-limiting conditions, its induction is controlled by two histidine kinases, DosS and DosT, and recent experimental evidence indicates DosS senses either molecular oxygen or a redox change. Under aerobic conditions, induction of the DosR regulon by DosS, but not DosT, was observed after the addition of ascorbate, a powerful cytochrome
c
reductant, demonstrating that DosS responds to a redox signal even in the presence of high oxygen tension. During hypoxic conditions, regulon induction was attenuated by treatment with compounds that occluded electron flow into the menaquinone pool or decreased the size of the menaquinone pool itself. Increased regulon expression during hypoxia was observed when exogenous menaquinone was added, demonstrating that the menaquinone pool is a limiting factor in regulon induction. Taken together, these data demonstrate that a reduced menaquinone pool directly or indirectly triggers induction of the DosR regulon via DosS. Biochemical analysis of menaquinones upon entry into hypoxic/anaerobic conditions demonstrated the disappearance of the unsaturated species and low-level maintenance of the mono-saturated menaquinone. Relative to the unsaturated form, an analog of the saturated form is better able to induce signaling via DosS and rescue inhibition of menaquinone synthesis and is less toxic. The menaquinone pool is central to the electron transport system (ETS) and therefore provides a mechanistic link between the respiratory state of the bacilli and DosS signaling. Although this report demonstrates that DosS responds to a reduced ETS, it does not rule out a role for oxygen in silencing signaling.
Role of Porins in Iron Uptake byMycobacterium smegmatis
Authors: Jones Christopher M. , Niederweis Michael 
Published: October 2010

ABSTRACTMany bacteria rely on siderophores to extract iron from the environment. However, acquisition of iron-loaded siderophores is dependent on high-affinity uptake systems that are not produced under high-iron conditions. The fact that bacteria are able to maintain iron homeostasis in the absence of siderophores indicates that alternative iron acquisition systems exist. It has been speculated that such low-affinity uptake of iron in Gram-negative bacteria includes diffusion of iron ions or chelates across the outer membrane through porins. The outer membrane of the saprophyticMycobacterium smegmatiscontains the Msp family of porins, which enable the diffusion of small and hydrophilic solutes, such as monosaccharides, amino acids, and phosphate. However, it is unknown how cations cross the outer membrane of mycobacteria. Here, we show that the Msp porins ofM. smegmatisare involved in the acquisition of soluble iron under high-iron conditions. Uptake of ferric ions by a triple porin mutant was reduced compared to wild-type (wt)M. smegmatis. An intracellular iron reporter indicated that derepression of iron-responsive genes occurs at higher iron concentrations in the porin mutant. This was consistent with the finding that the porin mutant produced more siderophores under low-iron conditions than wtM. smegmatis. In contrast, uptake of the exochelin MS, the main siderophore ofM. smegmatis, was not affected by the lack of porins, indicating that a specific outer membrane siderophore receptor exists. These results provide, to our knowledge, the first experimental evidence that general porins are indeed the outer membrane conduit of low-affinity iron acquisition systems in bacteria.
The Putative Assembly Factor CcoH Is Stably Associated with the
cbb
3
-Type Cytochrome Oxidase
Authors: Pawlik Grzegorz , Kulajta Carmen , Sachelaru Ilie , Schröder Sebastian , Waidner Barbara , Hellwig Petra , Daldal Fevzi , Koch Hans-Georg 
Published: October 2010

ABSTRACT

Cytochrome oxidases are perfect model substrates for analyzing the assembly of multisubunit complexes because the need for cofactor incorporation adds an additional level of complexity to their assembly.
cbb
3
-type cytochrome
c
oxidases (
cbb
3
-Cox) consist of the catalytic subunit CcoN, the membrane-bound
c
-type cytochrome subunits CcoO and CcoP, and the CcoQ subunit, which is required for
cbb
3
-Cox stability. Biogenesis of
cbb
3
-Cox proceeds via CcoQP and CcoNO subcomplexes, which assemble into the active
cbb
3
-Cox. Most bacteria expressing
cbb
3
-Cox also contain the
ccoGHIS
genes, which encode putative
cbb
3
-Cox assembly factors. Their exact function, however, has remained unknown. Here we analyzed the role of CcoH in
cbb
3
-Cox assembly and showed that CcoH is a single spanning-membrane protein with an N-terminus-out-C-terminus-in (N
out
-C
in
) topology. In its absence, neither the fully assembled
cbb
3
-Cox nor the CcoQP or CcoNO subcomplex was detectable. By chemical cross-linking, we demonstrated that CcoH binds primarily via its transmembrane domain to the CcoP subunit of
cbb
3
-Cox. A second hydrophobic stretch, which is located at the C terminus of CcoH, appears not to be required for contacting CcoP, but deleting it prevents the formation of the active
cbb
3
-Cox. This suggests that the second hydrophobic domain is required for merging the CcoNO and CcoPQ subcomplexes into the active
cbb
3
-Cox. Surprisingly, CcoH does not seem to interact only transiently with the
cbb
3
-Cox but appears to stay tightly associated with the active, fully assembled complex. Thus, CcoH behaves more like a bona fide subunit of the
cbb
3
-Cox than an assembly factor
per se
.
Instability ofackA(Acetate Kinase) Mutations and Their Effects on Acetyl Phosphate and ATP Amounts inStreptococcus pneumoniaeD39
Authors: Ramos-Montañez Smirla , Kazmierczak Krystyna M. , Hentchel Kristy L. , Winkler Malcolm E. 
Published: October 2010

ABSTRACTAcetyl phosphate (AcP) is a small-molecule metabolite that can act as a phosphoryl group donor for response regulators of two-component systems (TCSs). The serious human respiratory pathogenStreptococcus pneumoniae(pneumococcus) synthesizes AcP by the conventional pathway involving phosphotransacetylase and acetate kinase, encoded byptaandackA, respectively. In addition, pneumococcus synthesizes copious amounts of AcP and hydrogen peroxide (H2O2) by pyruvate oxidase, which is encoded byspxB. To assess possible roles of AcP in pneumococcal TCS regulation and metabolism, we constructed strains with combinations ofspxB,pta, andackAmutations and determined their effects on ATP, AcP, and H2O2production. Unexpectedly, ΔackAmutants were unstable and readily accumulated primary suppressor mutations in spxBor its positive regulator,spxR, thereby reducing H2O2and AcP levels, and secondary capsule mutations incps2Eorcps2C. ΔackAΔspxBmutants contained half the cellular amount of ATP as a ΔspxBorspxB+strain. Acetate addition and anaerobic growth experiments suggested decreased ATP, rather than increased AcP, as a reason that ΔackAmutants accumulatedspxBorspxRsuppressors, although experimental manipulation of the AcP amount was limited. This finding and other considerations suggest that coping with endogenously produced H2O2may require energy. Starting with a ΔspxBmutant, we constructed Δpta, ΔackA, and ΔptaΔackAmutants. Epistasis and microarray experiment results were consistent with a role for the SpxB-Pta-AckA pathway in expression of the regulons controlled by the WalRKSpn, CiaRHSpn, and LiaSRSpnTCSs involved in sensing cell wall status. However, AcP likely does not play a physiological role in TCS sensing inS. pneumoniae.
Genome of
Helicobacter pylori
Strain 908
Authors: Devi Singamaneni Haritha , Taylor Todd D. , Avasthi Tiruvayipati Suma , Kondo Shinji , Suzuki Yutaka , Megraud Francis , Ahmed Niyaz 
Published: October 2010

ABSTRACT

Helicobacter pylori
is a genetically diverse and coevolved pathogen inhabiting human gastric niches and leading to a spectrum of gastric diseases in susceptible populations. We describe the genome sequence of
H. pylori
908, which was originally isolated from an African patient living in France who suffered with recrudescent duodenal ulcer disease. The strain was found to be phylogenetically related to
H. pylori
J99, and its comparative analysis revealed several specific genome features and novel insertion-deletion and substitution events. The genome sequence revealed several strain-specific deletions and/or gain of genes exclusively present in HP908 compared with different sequenced genomes already available in the public domain. Comparative and functional genomics of HP908 and its subclones will be important in understanding genomic plasticity and the capacity to colonize and persist in a changing host environment.
Genome Sequence of the Biocontrol Agent
Pantoea vagans
Strain C9-1
Authors: Smits Theo H. M. , Rezzonico Fabio , Kamber Tim , Goesmann Alexander , Ishimaru Carol A. , Stockwell Virginia O. , Frey Jürg E. , Duffy Brion 
Published: October 2010

ABSTRACT

Pantoea vagans
is a Gram-negative enterobacterial plant epiphyte of a broad range of plants. Here we report the 4.89-Mb genome sequence of
P. vagans
strain C9-1 (formerly
Pantoea agglomerans
), which is commercially registered for biological control of fire blight, a disease of pear and apple trees caused by
Erwinia amylovora.
Genome Sequence of the Obligate Methanotroph
Methylosinus trichosporium
Strain OB3b
Authors: Stein Lisa Y. , Yoon Sukhwan , Semrau Jeremy D. , DiSpirito Alan A. , Crombie Andrew , Murrell J. Colin , Vuilleumier Stéphane , Kalyuzhnaya Marina G. , Op den Camp Huub J. M. , Bringel Françoise , Bruce D. , Cheng J.-F. , Copeland A. , Goodwin Lynne , Han Shunsheng , Hauser Loren , Jetten Mike S. M. , Lajus Aurélie , Land M. L. , Lapidus A. , Lucas S. , Médigue Claudine , Pitluck S. , Woyke Tanja , Zeytun Ahmet , Klotz Martin G. 
Published: October 2010

ABSTRACT

Methylosinus trichosporium
OB3b (for “oddball” strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from
M. trichosporium
OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the
M. trichosporium
OB3b genome is the first reported from a member of the
Methylocystaceae
family in the order
Rhizobiales
.
Genome Sequence of
Leuconostoc argentinum
KCTC 3773
Authors: Nam Seong-Hyeuk , Choi Sang-Haeng , Kang Aram , Kim Dong-Wook , Kim Ryong Nam , Kim Aeri , Park Hong-Seog 
Published: October 2010

ABSTRACT

Leuconostoc argentinum
is one of the most prevalent lactic acid bacteria present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of type strain KCTC 3773 of
Leuconostoc argentinum
(1,720,683 bp, with a G+C content of 42.9%), which consists of 98 large contigs (>100 bp in size).
Everyday ethics
Authors: Neale Madeleine 
Published: October 2010

THIS series gives readers the opportunity to consider and contribute to the discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved. In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, entitled ‘Substandard stockmanship’, is presented and discussed by Madeleine Neale. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue. Discussion of the dilemma ‘A patient abroad’, which was published in the June issue of In Practice, appears on page 417.The series is being coordinated by Siobhan Mullan, of the University of Bristol. It is hoped it will provide a framework that will help practices find solutions when facing similar dilemmas.
Medical surveillance programme for diisocyanate exposure
Authors: Labrecque Manon , Malo Jean-Luc , Alaoui Khadija M , Rabhi Khalil 
Published: October 2010

ObjectivesSurveillance programmes for occupational asthma should reduce the severity of asthma both at the time of diagnosis and after removal from exposure as well as costs related to functional impairment. The aim of this study was to compare the severity and cost of diisocyanate-induced occupational asthma in workers participating in a surveillance programme and in twice the number of workers diagnosed after being referred by their physician.MethodsAnswers to a self-administered questionnaire led to possible referral for further assessment that included methacholine testing and specific inhalation challenges as the gold standard for confirming occupational asthma.ResultsOf the 2897 workers who participated, 182 (6.3%) had a positive questionnaire. 79/182 (43%) were referred for further medical assessment and 20 had confirmed occupational asthma by specific inhalation testing. At the time of diagnosis, the 20 screened subjects had a mean PC20of 3.35 mg/ml as compared to 1.50 mg/ml (p=0.05) in the 66 controls. Two years after diagnosis and removal from exposure, the 20 subjects screened had a mean PC20of 4.81 mg/ml compared to 1.67 mg/ml (p=0.03) in controls. Clinical remission occurred in 34% of the screened group compared to 16% of the control group (p=0.02). The median costs for functional impairment were $C11 900 in screened subjects and $C19 600 in controls (p=0.04).ConclusionsSubjects with occupational asthma screened by a medical surveillance programme have a better outcome both at the time of diagnosis and 2 years after removal from exposure, with lower compensation costs compared to controls.
Traffic-related air pollution and incident asthma in a high-risk birth cohort
Authors: Carlsten Chris , Dybuncio Anne , Becker Allan , Chan-Yeung Moira , Brauer Michael 
Published: October 2010

ObjectivesThe risk of incident asthma and bronchial hyper-reactivity associated with early life exposure to traffic-related air pollution has not been fully elucidated. We aimed to evaluate the hypothesis that the risk of new onset asthma is positively associated with early exposure to traffic-related air pollution in a well-characterised high-risk birth cohort.MethodsInfants at high-risk for asthma were recruited for an intervention study. Birth year exposures to NO, NO2, black carbon and PM2.5were estimated by land use regression. At 7 years of age, asthma was assessed by a paediatric allergist and bronchial hyper-reactivity was measured by methacholine challenge. Associations between exposures and outcomes were analysed by stepwise multiple logistic regression, adjusted for potential confounding variables.ResultsExposure estimates were available for 184 children; 23 were diagnosed with asthma and 68 with bronchial hyper-reactivity. The IQR (4.1 μg/m3) of birth year PM2.5was associated with a significantly increased risk of asthma (OR 3.1, 95% CI 1.3 to 7.4) and with a trend to increased risk of bronchial hyper-reactivity. Similar findings were noted in association with NO and NO2, while black carbon did not appear to confer increased risk.ConclusionModest elevations in exposure to some traffic-related air pollutants during the year of birth are associated with new onset asthma assessed at age 7. That significant associations were revealed in spite of a limited sample size emphasises the strengths of a high-risk birth cohort model, along with individual air pollution exposure estimates and well-characterised data on covariates and outcomes.