bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse Functions for Six Glycosyltransferases in Caulobacter crescentus Cell Wall Assembly
Authors: Yakhnina Anastasiya A. , Gitai Zemer 
Published: August 2013

ABSTRACT

The essential process of peptidoglycan synthesis requires two enzymatic activities, transpeptidation and transglycosylation. While the PBP2 and PBP3 transpeptidases perform highly specialized functions that are widely conserved, the specific roles of different glycosyltransferases are poorly understood. For example,
Caulobacter crescentus
encodes six glycosyltransferase paralogs of largely unknown function. Using genetic analyses, we found that
Caulobacter
glycosyltransferases are primarily redundant but that PbpX is responsible for most of the essential glycosyltransferase activity. Cells containing PbpX as their sole glycosyltransferase are viable, and the loss of
pbpX
leads to a general defect in the integrity of the cell wall structure even in the presence of the other five glycosyltransferases. However, neither PbpX nor any of its paralogs is required for the specific processes of cell elongation or division, while the cell wall synthesis required for stalk biogenesis is only partially disrupted in several of the glycosyltransferase mutants. Despite their genetic redundancy,
Caulobacter
glycosyltransferases exhibit different subcellular localizations. We suggest that these enzymes have specialized roles and normally function in distinct subcomplexes but retain the ability to substitute for one another so as to ensure the robustness of the peptidoglycan synthesis process.
Identification and Characterization of RibN, a Novel Family of Riboflavin Transporters from Rhizobium leguminosarum and Other Proteobacteria
Authors: García Angulo Víctor A. , Bonomi Hernán R. , Posadas Diana M. , Serer María I. , Torres Alfredo G. , Zorreguieta Ángeles , Goldbaum Fernando A. 
Published: August 2013

ABSTRACT

Rhizobia are symbiotic bacteria able to invade and colonize the roots of legume plants, inducing the formation of nodules, where bacteria reduce atmospheric nitrogen (N
2
) to ammonia (NH
3
). Riboflavin availability influences the capacity of rhizobia to survive in the rhizosphere and to colonize roots. In this study, we identified the
RL1692
gene of
Rhizobium leguminosarum
downstream of a flavin mononucleotide (FMN) riboswitch.
RL1692
encodes a putative transmembrane permease with two EamA domains. The presence of an FMN riboswitch regulating a transmembrane protein is usually observed in riboflavin transporters, suggesting that RL1692 may be involved in riboflavin uptake. The product of
RL1692
, which we named RibN, is conserved in members of the alpha-, beta-, and gammaproteobacteria and shares no significant identity with any riboflavin transporter previously identified. In this work, we show that RibN is localized in the membrane cellular fraction and its expression is downregulated by riboflavin. By heterologous expression in a
Brucella abortus
mutant auxotrophic for riboflavin, we demonstrate that RibN possesses flavin transport activity. Similarly, we also demonstrate that RibN orthologues from
Ochrobactrum anthropi
and
Vibrio cholerae
(which lacks the FMN riboswitch) are able to transport riboflavin. An
R. leguminosarum ribN
null mutant exhibited lower nodule occupancy levels in pea plants during symbiosis assays. Thus, we propose that RibN and its homologues belong to a novel family of riboflavin transporters. This work provides the first experimental description of riboflavin transporters in Gram-negative bacteria.
Control of the Escherichia coli Sialoregulon by Transcriptional Repressor NanR
Authors: Kalivoda Kathryn A. , Steenbergen Susan M. , Vimr Eric R. 
Published: August 2013

ABSTRACT

NanR, one of >8,500 GntR superfamily helix-turn-helix transcriptional regulators, controls expression of the genes required for catabolism of sialic acids in
Escherichia coli
. It is predicted to do the same in related bacteria harboring orthologs of
nanR
. The sialic acids are a family of over 40 naturally occurring nine-carbon keto-sugar acids found mainly in the animal lineage, which includes starfish to humans in the deuterostome lineage. Sialic acids function in development, immunity, protein localization and stability, and homeostasis. They also serve as microbial carbon and nitrogen sources and ligands for cell recognition during host colonization. The importance of microbial sialic acid metabolism for host-microbe interactions has made it a target for therapeutic development. Exploiting this target depends on understanding sialometabolic pathways in a wide range of evolutionarily distinct bacteria. Here, we show by transcriptome, genetic, and biochemical analyses that the most common sialic acid,
N
-acetylneuraminate, induces the
nanATEK-yhcH
,
yjhATS
(
nanCMS
), and
yjhBC
operons by directly inactivating NanR, converting the predominantly dimeric form of the repressor to an inactive monomer of approximately 30-kDa. Additionally, other results identify critical amino acid residues and nucleotides in the regulator and operator, respectively. The combined results better define how sialic acids, acting through NanR, affect the metabolic flux of an important group of host-derived metabolites. Thus,
E. coli
serves as a valuable model for understanding sialocatabolic pathways in bacteria.
Nitrite Reductase NirBD Is Induced and Plays an Important Role during
In Vitro
Dormancy of Mycobacterium tuberculosis
Authors: Akhtar Shamim , Khan Arshad , Sohaskey Charles D. , Jagannath Chinnaswamy , Sarkar Dhiman 
Published: August 2013

ABSTRACT

Mycobacterium tuberculosis
is one of the strongest reducers of nitrate among all mycobacteria. Reduction of nitrate to nitrite, mediated by nitrate reductase (NarGHJI) of
M. tuberculosis
, is induced during the dormant stage, and the enzyme has a respiratory function in the absence of oxygen. Nitrite reductase (NirBD) is also functional during aerobic growth when nitrite is the sole nitrogen source. However, the role of NirBD-mediated nitrite reduction during the dormancy is not yet characterized. Here, we analyzed nitrite reduction during aerobic growth as well as in a hypoxic dormancy model of
M. tuberculosis in vitro
. When nitrite was used as the sole nitrogen source in the medium, the organism grew and the reduction of nitrite was evident in both hypoxic and aerobic cultures of
M. tuberculosis
. Remarkably, the hypoxic culture of
M. tuberculosis
, compared to the aerobic culture, showed 32- and 4-fold-increased expression of nitrite reductase (NirBD) at the transcription and protein levels, respectively. More importantly, a
nirBD
mutant of
M. tuberculosis
was unable to reduce nitrite and compared to the wild-type (WT) strain had a >2-log reduction in viability after 240 h in the Wayne model of hypoxic dormancy. Dependence of
M. tuberculosis
on nitrite reductase (NirBD) was also seen in a human macrophage-based dormancy model where the
nirBD
mutant was impaired for survival compared to the WT strain. Overall, the increased expression and essentiality of nitrite reductase in the
in vitro
dormancy models suggested that NirBD-mediated nitrite reduction could be critical during the persistent stage of
M. tuberculosis
.
The Putative Enoyl-Coenzyme A Hydratase DspI Is Required for Production of the Pseudomonas aeruginosa Biofilm Dispersion Autoinducer
cis
-2-Decenoic Acid
Authors: Amari Diana T. , Marques Cláudia N. H. , Davies David G. 
Published: August 2013

ABSTRACT

In the present study, we report the identification of a putative enoyl-coenzyme A (CoA) hydratase/isomerase that is required for synthesis of the biofilm dispersion autoinducer
cis
-2-decenoic acid in the human pathogen
Pseudomonas aeruginosa
. The protein is encoded by PA14_54640 (PA0745), named
dspI
for
d
i
sp
ersion
i
nducer. The gene sequence for this protein shows significant homology to RpfF in
Xanthomonas campestris
. Inactivation of
dspI
was shown to abolish biofilm dispersion autoinduction in continuous cultures of
P. aeruginosa
and resulted in biofilms that were significantly greater in thickness and biomass than those of the parental wild-type strain. Dispersion was shown to be inducible in
dspI
mutants by the exogenous addition of synthetic
cis
-2-decenoic acid or by complementation of Δ
dspI in trans
under the control of an arabinose-inducible promoter. Mutation of
dspI
was also shown to abolish
cis
-2-decenoic acid production, as revealed by gas chromatography-mass spectrometry (GC-MS) analysis of cell-free spent culture medium. The transcript abundance of
dspI
correlated with cell density, as determined by quantitative reverse transcriptase (RT) PCR. This regulation is consistent with the characterization of
cis
-2-decenoic acid as a cell-to-cell communication molecule that regulates biofilm dispersion in a cell density-dependent manner.
ppGpp Metabolism Is Involved in Heterocyst Development in the Cyanobacterium Anabaena sp. Strain PCC 7120
Authors: Zhang Shao-Ran , Lin Gui-Ming , Chen Wen-Li , Wang Li , Zhang Cheng-Cai 
Published: August 2013

ABSTRACT

When deprived of a combined-nitrogen source in the growth medium, the filamentous cyanobacterium
Anabaena
sp. PCC 7120 (
Anabaena
) can form heterocysts capable of nitrogen fixation. The process of heterocyst differentiation takes about 20 to 24 h, during which extensive metabolic and morphological changes take place. Guanosine tetraphosphate (ppGpp) is the signal of the stringent response that ensures cell survival by adjusting major cellular activities in response to nutrient starvation in bacteria, and ppGpp accumulates at the early stage of heterocyst differentiation (J. Akinyanju, R. J. Smith, FEBS Lett. 107:173–176, 1979; J Akinyanju, R. J. Smith, New Phytol. 105:117–122, 1987). Here we show that
all1549
(here designated

rel
ana

) in
Anabaena
, homologous to
relA/spoT
, is upregulated in response to nitrogen deprivation and predominantly localized in vegetative cells. The disruption of

rel
ana

strongly affects the synthesis of ppGpp, and the resulting mutant,
all1549
Ωsp/sm, fails to form heterocysts and to grow in the absence of a combined-nitrogen source. This phenotype can be complemented by a wild-type copy of

rel
ana

. Although the upregulation of
hetR
is affected in the mutant, ectopic overexpression of
hetR
cannot rescue the phenotype. However, we found that the mutant rapidly loses its viability, within a time window of 3 to 6 h, following the deprivation of combined nitrogen. We propose that ppGpp plays a major role in rebalancing the metabolic activities of the cells in the absence of the nitrogen source supply and that this regulation is necessary for filament survival and consequently for the success of heterocyst differentiation.
Interaction of Streptococcus mutans YidC1 and YidC2 with Translating and Nontranslating Ribosomes
Authors: Wu Zht Cheng , de Keyzer Jeanine , Berrelkamp-Lahpor Greetje A. , Driessen Arnold J. M. 
Published: August 2013

ABSTRACT

The YidC/OxaI/Alb3 family of membrane proteins is involved in the biogenesis of integral membrane proteins in bacteria, mitochondria, and chloroplasts. Gram-positive bacteria often contain multiple YidC paralogs that can be subdivided into two major classes, namely, YidC1 and YidC2. The
Streptococcus mutans
YidC1 and YidC2 proteins possess C-terminal tails that differ in charges (+9 and + 14) and lengths (33 and 61 amino acids). The longer YidC2 C terminus bears a resemblance to the C-terminal ribosome-binding domain of the mitochondrial OxaI protein and, in contrast to the shorter YidC1 C terminus, can mediate the interaction with mitochondrial ribosomes. These observations have led to the suggestion that YidC1 and YidC2 differ in their abilities to interact with ribosomes. However, the interaction with bacterial translating ribosomes has never been addressed. Here we demonstrate that
Escherichia coli
ribosomes are able to interact with both YidC1 and YidC2. The interaction is stimulated by the presence of a nascent membrane protein substrate and abolished upon deletion of the C-terminal tail, which also abrogates the YidC-dependent membrane insertion of subunit c of the F
1
F
0
-ATPase into the membrane. It is concluded that both YidC1 and YidC2 interact with ribosomes, suggesting that the modes of membrane insertion by these membrane insertases are similar.
The MerR-Like Regulator BrlR Impairs Pseudomonas aeruginosa Biofilm Tolerance to Colistin by Repressing PhoPQ
Authors: Chambers Jacob R. , Sauer Karin 
Published: August 2013

ABSTRACT

While the MerR-like transcriptional regulator BrlR has been demonstrated to contribute to
Pseudomonas aeruginosa
biofilm tolerance to antimicrobial agents known as multidrug efflux pump substrates, the role of BrlR in resistance to cationic antimicrobial peptides (CAP), which is based on reduced outer membrane susceptibility, is not known. Here, we demonstrate that inactivation of
brlR
coincided with increased resistance of
P. aeruginosa
to colistin, while overexpression of
brlR
resulted in increased susceptibility.
brlR
expression correlated with reduced transcript abundances of
phoP
,
phoQ
,
pmrA
,
pmrB
, and
arnC
. Inactivation of
pmrA
and
pmrB
had no effect on the susceptibility of
P. aeruginosa
biofilms to colistin, while inactivation of
phoP
and
phoQ
rendered biofilms more susceptible than the wild type. The susceptibility phenotype of Δ
phoP
biofilms to colistin was comparable to that of
P. aeruginosa
biofilms overexpressing
brlR
. BrlR was found to directly bind to
oprH
promoter DNA of the
oprH-phoPQ
operon. BrlR reciprocally contributed to colistin and tobramycin resistance in
P. aeruginosa
PAO1 and CF clinical isolates, with overexpression of
brlR
resulting in increased tobramycin MICs and increased tobramycin resistance but decreased colistin MICs and increased colistin susceptibility. The opposite trend was observed upon
brlR
inactivation. The difference in susceptibility to colistin and tobramycin was eliminated by combination treatment of biofilms with both antibiotics. Our findings establish BrlR as an unusual member of the MerR family, as it not only functions as a multidrug transport activator, but also acts as a repressor of
phoPQ
expression, thus suppressing colistin resistance.
A Novel Protein Protects Bacterial Iron-Dependent Metabolism from Nitric Oxide
Authors: Stern Andrew M. , Liu Binbin , Bakken Lars R. , Shapleigh James P. , Zhu Jun 
Published: August 2013

ABSTRACTReactive nitrogen species (RNS), in particular nitric oxide (NO), are toxic to bacteria, and bacteria have mechanisms to allow growth despite this stress. Understanding how bacteria interact with NO is essential to understanding bacterial physiology in many habitats, including pathogenesis; however, many targets of NO and enzymes involved in NO resistance remain uncharacterized. We performed for the first time a metabolomic screen on NO-treated and -untreated bacteria to define broadly the effects of NO on bacterial physiology, as well as to identify the function of NnrS, a previously uncharacterized enzyme involved in defense against NO. We found many known and novel targets of NO. We also found that iron-sulfur cluster enzymes were preferentially inhibited in a strain lacking NnrS due to the formation of iron-NO complexes. We then demonstrated that NnrS is particularly important for resistance to nitrosative stress under anaerobic conditions. Our data thus reveal the breadth of the toxic effects of NO on metabolism and identify the function of an important enzyme in alleviating this stress.
Predictive accuracy of triage nurses evaluation in risk stratification of syncope in the emergency department
Authors: Bonzi M , Fiorelli E M , Angaroni L , Furlan L , Solbiati M , Colombo C , Dipaola F , Montano N , Furlan R , Costantino G 
Published: August 2013

BackgroundSyncope is a common clinical problem that accounts for 1–3% of all emergency department (ED) visits. Its prognosis is extremely variable with a 1-year mortality that may reach 30%. There are no available data about the accuracy of nursing triage in identifying high-risk syncope. The aim of our study was to evaluate the predictive accuracy of nursing triage in identifying high-risk syncope.MethodsWe conducted a retrospective study on 678 consecutive patients who presented with syncope at four EDs. For each patient, nursing triage, comorbidities, clinical features and adverse events that occurred both in the ED and at 10-day follow-up were assessed. Adverse events included death, readmission to ED, need for major therapeutic procedures, cardiopulmonary resuscitation, intensive care unit admittance, acute antiarrhythmic therapy and major causes of syncope identified during the ED evaluation. Predictive accuracy of nursing triage was evaluated.ResultsWe observed a total of 55 (8.1%) adverse events. Eight of them (9.4%) occurred among the 85 patients who were identified as high priority by nursing triage. Sensitivity (Sn) and specificity (Sp) of urgent nursing triage in identifying adverse outcomes in the ED (19 patients) were 21% (95% CI 3% to 39%) and 88% (95% CI 85% to 90%), while the positive likelihood ratio (LR+) and negative likelihood ratio (LR−) were 1.7 and 0.9, respectively. Sn and Sp for 10-day adverse events were 15% (95% CI 5% to 24%) and 88% (95% CI 85% to 90%), respectively, with a LR+ of 1.18 and a LR− of 0.98.ConclusionsNursing triage was characterised by a low predictive accuracy in identifying high-risk individuals.
Clinical significance of micropapillary urothelial carcinoma of the upper urinary tract
Authors: Sung Hyun Hwan , Cho Junhun , Kwon Ghee Young , Jeon Hwang Gyun , Jeong Byong Chang , Seo Seong Il , Jeon Seong Soo , Choi Han-Yong , Lee Hyun Moo 
Published: August 2013

BackgroundThe aim of this study was to improve understanding of the characteristics of micropapillary urothelial carcinoma (MPUC) in the renal pelvis and ureter, and to compare oncological outcomes between MPUC and non-MPUC.MethodsFrom September 1994 to October 2010, 418 patients underwent nephroureterectomy with bladder excision due to presumed urothelial carcinoma. Pathological review of all specimens was done by one uropathologist. Perioperative data from these patients were reviewed retrospectively. Patients were divided into MPUC and non-MPUC groups. Oncological outcomes were compared between the two groups via progression-free survival (PFS) and cancer-specific survival (CSS) rates.ResultsA total of 386 patients were included in the study. Of these, seven patients (1.81%) had MPUC. The median follow-up duration was 39.0 months (IQR range 21.1–70.6). All MPUC patients were men and had lymphovascular invasion, and six patients (85.7%) had grade III and T3 disease. On univariable analysis, MPUC showed significantly worse prognosis with regard to disease progression (p<0.001). In the subgroup analysis confined to T3 or T4 disease, MPUC showed worse prognosis than non-MPUC in terms of PFS and CSS, respectively (p<0.05). In the multivariable model, MPUC still remained a statistically significant independent predictor for PFS (HR (95% CI)=3.85 (1.59–9.32), p=0.003). MPUC was associated with poorer CSS than non-MPUC (p<0.001).ConclusionsWe have observed that upper tract MPUC is associated with poor oncological outcomes in terms of PFS and CSS. MPUC was an independent prognostic factor for PFS in multivariable analysis.
Validating the 5Fs mnemonic for cholelithiasis: time to include family history
Authors: Bass Gary , Gilani S Nadia S , Walsh Thomas N , Leader Frank 
Published: August 2013

Abstract

Background
The time-honoured mnemonic of ‘5Fs’ is a reminder to students that patients with upper abdominal pain and who conform to a profile of ‘fair, fat, female, fertile and forty’ are likely to have cholelithiasis. We feel, however, that a most important ‘F’—that for ‘family history’—is overlooked and should be introduced to enhance the value of a useful aide memoire.

Methods
To assess the usefulness of each of the existing factors of a popular mnemonic, 398 patients admitted with upper abdominal pain between March 2009 and April 2010 were studied. The clinical features expressed in the cholelithiasis mnemonic in patients with sonographic evidence of cholelithiasis were compared with those of patients without.

Findings
In the cholelithiasis group, significantly more patients were women (150/198 (75.8%) vs 111/200 (55.5%), p&lt;0.001), fair (144/198 (62.9%) vs 54/200 (32.1%), (p&lt;0.001)), fertile (135/198 (68.2%) vs 50/200 (25%) (p&lt;0.001)) and had a body mass index &gt;30 (56/198 (28.3%) vs 19/200 (9.5%) (p&lt;0.001)) compared with controls; but age over 40 years did not predict cholelithiasis (82/198 (41.4%) vs 79/200 (39.5%) (p=0.697)). In the cholelithiasis group, 78/198 (39.4%) had a family history in at least one first-degree relative, compared with 27/200 (13.5%) of controls, (p&lt;0.001). Where the phenotypic elements of the history existed in combination, that patient was found to be at an increased risk of cholelithiasis.

Interpretation
Our study found that the validated ‘students’ 5Fs’ mnemonic retains a role in clinical diagnosis of patients suspected of cholelithiasis but the factor ‘familial’ should be substituted for ‘forty’ in recognition of the role of inheritance and the changing demographics of gallstone incidence.
Pathogen profile in men with inflammation of paraurethral glands
Authors: Fan Wenge , Zhang Qingsong , Jiang Tingwang 
Published: August 2013

ObjectiveTo investigate the pathogen profile in men with inflammation of the paraurethral glands.MethodsWe enrolled 40 patients with first-onset, drug-naive inflammation of the paraurethral glands. Discharge from the lesions was collected for Gram staining. Microscopy was performed for screening for trichomonads and detecting Gram-negative intracellular diplococci within phagocytes. Cultures for detection ofNeisseria gonorrhoeae,Ureaplasma urealyticumand other bacteria, andChlamydia-trachomatis-associated antigens were performed. PCR was conducted for herpes simplex virus type 1 or 2.ResultsFrom these 40 patients, there were nine microbial species, which included Gram-negative bacteria (23 cases, 54.8%), Gram-positive bacteria (15 cases, 35.7%) and other pathogens (4 cases, 9.5%). The top three pathogens were gonococci (38.1%),Staphylococcus aureus(16.7%) andEscherichia coli(14.3%).ConclusionsInflammation of paraurethral glands in men may be caused by a variety of pathogens and not just by gonococcal infection.