bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex regulation of the global regulatory gene csrA: CsrA‐mediated translational repression, transcription from five promoters by Eσ70 and EσS, and indirect transcriptional activation by CsrA
Authors: Yakhnin Helen , Yakhnin Alexander V. , Baker Carol S. , Sineva Elena , Berezin Igor , Romeo Tony , Babitzke Paul 
Published: June 2011

SummaryCsrA of Escherichia coli is an RNA‐binding protein that globally regulates gene expression by repressing translation and/or altering the stability of target transcripts. Here we explored mechanisms that control csrA expression. Four CsrA binding sites were predicted upstream of the csrA initiation codon, one of which overlapped its Shine–Dalgarno sequence. Results from gel shift, footprint, toeprint and in vitro translation experiments indicate that CsrA binds to these four sites and represses its own translation by directly competing with 30S ribosomal subunit binding. Experiments were also performed to examine transcription of csrA. Primer extension, in vitro transcription and in vivo expression studies identified two σ70‐dependent (P2 and P5) and two σS‐dependent (P1 and P3) promoters that drive transcription of csrA. Additional primer extension studies identified a fifth csrA promoter (P4). Transcription from P3, which is indirectly activated by CsrA, is primarily responsible for increased csrA expression as cells transition from exponential to stationary‐phase growth. Taken together, our results indicate that regulation of csrA expression occurs by a variety of mechanisms, including transcription from multiple promoters by two sigma factors, indirect activation of its own transcription, as well as direct repression of its own translation.
The novel Pseudomonas aeruginosa two‐component regulator BfmR controls bacteriophage‐mediated lysis and DNA release during biofilm development through PhdA
Authors: Petrova Olga E. , Schurr Jill R. , Schurr Michael J. , Sauer Karin 
Published: June 2011

SummaryBiofilms are surface‐adhered bacterial communities encased in an extracellular matrix composed of polysaccharides, proteins, and extracellular (e)DNA, with eDNA required for biofilm formation and integrity. Here we demonstrate that eDNA release is controlled by BfmR, a regulator essential for Pseudomonas aeruginosa biofilm development. Expression of bfmR coincided with localized cell death and DNA release, and could be stimulated by conditions resulting in membrane perturbation and cell lysis. ΔbfmR mutant biofilms demonstrated increased cell lysis and eDNA release suggesting BfmR to suppress, but not eliminate, these processes. Genome‐wide transcriptional profiling indicated that BfmR was required for repression of genes associated with bacteriophage assembly and bacteriophage‐mediated lysis. Chromatin immunoprecipitation analysis of direct BfmR targets identified the promoter of PA0691, termed here phdA, encoding a previously undescribed homologue of the prevent‐host‐death (Phd) family of proteins. Lack of phdA expression coincided with impaired biofilm development and increased cell death, a phenotype comparable to ΔbfmR. Expression of phdA in ΔbfmR restored eDNA release, cell lysis and biofilm formation to wild‐type levels, with phdA overexpression promoting resistance to the superinfective bacteriophage Pf4, detected only in biofilms. Therefore, we propose that BfmR regulates biofilm development by limiting bacteriophage‐mediated lysis and thus, eDNA release, via PhdA.
Bacitracin and nisin resistance in Staphylococcus aureus: a novel pathway involving the BraS/BraR two‐component system (SA2417/SA2418) and both the BraD/BraE and VraD/VraE ABC transporters
Authors: Hiron Aurélia , Falord Mélanie , Valle Jaione , Débarbouillé Michel , Msadek Tarek 
Published: June 2011

SummaryTwo‐component systems (TCSs) are key regulatory pathways allowing bacteria to adapt their genetic expression to environmental changes. Bacitracin, a cyclic dodecylpeptide antibiotic, binds to undecaprenyl pyrophosphate, the lipid carrier for cell wall precursors, effectively inhibiting peptidoglycan biosynthesis. We have identified a novel and previously uncharacterized TCS in the major human pathogen Staphylococcus aureus that we show to be essential for bacitracin and nisin resistance: the BraS/BraR system (Bacitracin resistance associated; SA2417/SA2418). The braRS genes are located immediately upstream from genes encoding an ABC transporter, accordingly designated BraDE. We have shown that the BraSR/BraDE module is a key bacitracin and nisin resistance determinant in S. aureus. In the presence of low antibiotic concentrations, BraSR activate transcription of two operons encoding ABC transporters: braDE and vraDE. We identified a highly conserved imperfect palindromic sequence upstream from the braDE and vraDE promoter sequences, essential for their transcriptional activation by BraSR, suggesting it is the likely BraR binding site. We demonstrated that the two ABC transporters play distinct and original roles in antibiotic resistance: BraDE is involved in bacitracin sensing and signalling through BraSR, whereas VraDE acts specifically as a detoxification module and is sufficient to confer bacitracin and nisin resistance when produced on its own. We show that these processes require functional BraD and VraD nucleotide‐binding domain proteins, and that the large extracellular loop of VraE confers its specificity in bacitracin resistance. This is the first example of a TCS associated with two ABC transporters playing separate roles in signal transduction and antibiotic resistance.
Hsp31 of Escherichia coli K‐12 is glyoxalase III
Authors: Subedi Krishna P. , Choi Dongwook , Kim Insook , Min Bumchan , Park Chankyu 
Published: June 2011

SummaryHsp31 encoded by hchA is known as a heat‐inducible molecular chaperone. Although structure studies revealed that Hsp31 has a putative catalytic triad consisting of Asp‐214, His‐186 and Cys‐185, its enzymatic function, besides weak amino‐peptidase activity, is still unknown. We found that Hsp31 displays glyoxalase activity that catalyses the conversion of methylglyoxal (MG) to d‐lactate without an additional cofactor. The glyoxalase activity was completely abolished in the hchA‐deficient strain, confirming the relationship between the hchA gene and its enzymatic activity in vivo. Hsp31 exhibits Michaelis–Menten kinetics for substrates MG with Km and kcat of 1.43 ± 0.12 mM and 156.9 ± 5.5 min−1 respectively. The highest glyoxalase activity was found at 35–40°C and pH of 6.0–8.0, and the activity was significantly inhibited by Cu2+, Fe3+ and Zn2+. Mutagenesis studies based on our evaluation of conserved catalytic residues revealed that the Cys‐185 and Glu‐77 were essential for catalysis, whereas His‐186 was less crucial for enzymatic function, although it participates in the catalytic process. The stationary‐phase Escherichia coli cells became more susceptible to MG when hchA was deleted, which was complemented by an expression of plasmid‐encoded hchA. Furthermore, an accumulation of intracellular MG was observed in hchA‐deficient strains.
ArsAB, a novel enzyme from Sporomusa ovata activates phenolic bases for adenosylcobamide biosynthesis
Authors: Chan Chi Ho , Escalante‐Semerena Jorge C. 
Published: June 2011

SummaryIn the homoacetogenic bacterium Sporomusa ovata, phenol and p‐cresol are converted into α‐ribotides, which are incorporated into biologically active cobamides (Cbas) whose lower ligand bases do not form axial co‐ordination bonds with the cobalt ion of the corrin ring. Here we report the identity of two S. ovata genes that encode an enzyme that transfers the phosphoribosyl group of nicotinate mononucleotide (NaMN) to phenol or p‐cresol, yielding α‐O‐glycosidic ribotides. The alluded genes were named arsA and arsB (for alpha‐ribotide synthesis), arsA and arsB were isolated from a genomic DNA library of S. ovata. A positive selection strategy using an Escherichia coli strain devoid of NaMN:5,6‐dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) activity was used to isolate a fragment of S. ovata DNA that contained arsA and arsB, whose nucleotide sequences overlapped by 8 bp. SoArsAB was isolated to homogeneity, shown to be functional as a heterodimer, and to have highest activity at pH 9. SoArsAB also activated DMB to its α‐N‐glycosidic ribotide. Previously characterized CobT‐like enzymes activate DMB but do not activate phenolics. NMR spectroscopy was used to confirm the incorporation of phenol into the cobamide, and mass spectrometry was used to identify SoArsAB reaction products.
Characterization of DNA‐binding sequences for CcaR in the cephamycin–clavulanic acid supercluster of Streptomyces clavuligerus
Authors: Santamarta I. , López‐García M. T. , Kurt A. , Nárdiz N. , Álvarez‐Álvarez R. , Pérez‐Redondo R. , Martín J. F. , Liras P. 
Published: June 2011

SummaryRT‐PCR analysis of the genes in the clavulanic acid cluster revealed three transcriptional polycistronic units that comprised the ceaS2–bls2–pah2–cas2, cyp–fd–orf12–orf13 and oppA2–orf16 genes, whereas oat2, car, oppA1, claR, orf14, gcaS and pbpA were expressed as monocistronic transcripts. Quantitative RT‐PCR of Streptomyces clavuligerus ATCC 27064 and the mutant S. clavuligerus ccaR::aph showed that, in the mutant, there was a 1000‐ to 10 000‐fold lower transcript level for the ceaS2 to cas2 polycistronic transcript that encoded CeaS2, the first enzyme of the clavulanic acid pathway that commits arginine to clavulanic acid biosynthesis. Smaller decreases in expression were observed in the ccaR mutant for other genes in the cluster. Two‐dimensional electrophoresis and MALDI‐TOF analysis confirmed the absence in the mutant strain of proteins CeaS2, Bls2, Pah2 and Car that are required for clavulanic acid biosynthesis, and CefF and IPNS that are required for cephamycin biosynthesis. Gel shift electrophoresis using recombinant r‐CcaR protein showed that it bound to the ceaS2 and claR promoter regions in the clavulanic acid cluster, and to the lat, cefF, cefD–cmcI and ccaR promoter regions in the cephamycin C gene cluster. Footprinting experiments indicated that triple heptameric conserved sequences were protected by r‐CcaR, and allowed identification of heptameric sequences as CcaR binding sites.
Two autonomous structural modules in the fimbrial shaft adhesin FimA mediate Actinomyces interactions with streptococci and host cells during oral biofilm development
Authors: Mishra Arunima , Devarajan Bharanidharan , Reardon Melissa E. , Dwivedi Prabhat , Krishnan Vengadesan , Cisar John O. , Das Asis , Narayana Sthanam V. L. , Ton‐That Hung 
Published: June 2011

SummaryBy combining X‐ray crystallography and modelling, we describe here the atomic structure of distinct adhesive moieties of FimA, the shaft fimbrillin of Actinomyces type 2 fimbriae, which uniquely mediates the receptor‐dependent intercellular interactions between Actinomyces and oral streptococci as well as host cells during the development of oral biofilms. The FimA adhesin is built with three IgG‐like domains, each of which harbours an intramolecular isopeptide bond, previously described in several Gram‐positive pilins. Genetic and biochemical studies demonstrate that although these isopeptide bonds are dispensable for fimbrial assembly, cell–cell interactions and biofilm formation, they contribute significantly to the proteolytic stability of FimA. Remarkably, FimA harbours two autonomous adhesive modules, which structurally resemble the Staphylococcus aureus Cna B domain. Each isolated module can bind the plasma glycoprotein asialofetuin as well as the polysaccharide receptors present on the surface of oral streptococci and epithelial cells. Thus, FimA should serve as an excellent paradigm for the development of therapeutic strategies and elucidating the precise molecular mechanisms underlying the interactions between cellular receptors and Gram‐positive fimbriae.
Antimicrobial peptide sensing and detoxification modules: unravelling the regulatory circuitry of Staphylococcus aureus
Authors: Gebhard Susanne , Mascher Thorsten 
Published: June 2011

SummaryInvestigations into the resistance mechanisms of Firmicutes bacteria against antimicrobial peptides have revealed unique resistance modules comprised of an unusual type of ATP‐binding cassette (ABC) transporter, paired with a two‐component regulatory system. In these systems, the ABC‐transporter is not only involved in detoxification of the peptides, but also in their detection and resulting regulation of gene expression. The manuscript by Hiron et al. (2011) published in this issue describes an intriguing complexity of regulatory circuits and division of labour between the three paralogous modules in Staphylococcus aureus, providing important mechanistic insights and new perspectives for future investigations of these unique systems.
Pervasive post‐transcriptional control of genes involved in amino acid metabolism by the Hfq‐dependent GcvB small RNA
Authors: Sharma Cynthia M. , Papenfort Kai , Pernitzsch Sandy R. , Mollenkopf Hans‐Joachim , Hinton Jay C. D. , Vogel Jörg 
Published: June 2011

SummaryGcvB is one of the most highly conserved Hfq‐associated small RNAs in Gram‐negative bacteria and was previously reported to repress several ABC transporters for amino acids. To determine the full extent of GcvB‐mediated regulation in Salmonella, we combined a genome‐wide experimental approach with biocomputational target prediction. Comparative pulse expression of wild‐type versus mutant sRNA variants revealed that GcvB governs a large post‐transcriptional regulon, impacting ∼1% of all Salmonella genes via its conserved G/U‐rich domain R1. Complementary predictions of C/A‐rich binding sites in mRNAs and gfp reporter fusion experiments increased the number of validated GcvB targets to more than 20, and doubled the number of regulated amino acid transporters. Unlike the previously described targeting via the single R1 domain, GcvB represses the glycine transporter CycA by exceptionally redundant base‐pairing. This novel ability of GcvB is focused upon the one target that could feedback‐regulate the glycine‐responsive synthesis of GcvB. Several newly discovered mRNA targets involved in amino acid metabolism, including the global regulator Lrp, question the previous assumption that GcvB simply acts to limit unnecessary amino acid uptake. Rather, GcvB rewires primary transcriptional control circuits and seems to act as a distinct regulatory node in amino acid metabolism.
A quantitative study of the neuropathology of 32 sporadic and familial cases of frontotemporal lobar degeneration with TDP‐43 proteinopathy (FTLD‐TDP)
Authors: Armstrong R. A. , Carter D. , Cairns N. J. 
Published: June 2011

R. A. Armstrong, D. Carter and N. J. Cairns (2012) Neuropathology and Applied Neurobiology38, 25–38A quantitative study of the neuropathology of 32 sporadic and familial cases of frontotemporal lobar degeneration with TDP‐43 proteinopathy (FTLD‐TDP)Aims: To further characterize the neuropathology of the heterogeneous molecular disorder frontotemporal lobar degeneration (FTLD) with transactive response (TAR) DNA‐binding protein of 43 kDa (TDP‐43) proteinopathy (FTLD‐TDP). Methods: We quantified the neuronal cytoplasmic inclusions, glial inclusions, neuronal intranuclear inclusions, dystrophic neurites, surviving neurones, abnormally enlarged neurones, and vacuoles in regions of the frontal and temporal lobe using a phosphorylation‐independent TDP‐43 antibody in 32 cases of FTLD‐TDP comprising sporadic and familial cases, with associated pathology such as hippocampal sclerosis (HS) or Alzheimer's disease (AD), and four neuropathological subtypes using TDP‐43 immunohistochemistry. Analysis of variance (anova) was used to compare differences between the various groups of cases. Results: These data from FTLD‐TDP cases demonstrate quantitative differences in pathological features between: (i) regions of the frontal and temporal lobe; (ii) upper and lower cortex; (iii) sporadic and progranulin (GRN) mutation cases; (iv) cases with and without AD or HS; and (v) between assigned subtypes. Conclusions: The data confirm that the dentate gyrus is a major site of neuropathology in FTLD‐TDP and that most laminae of the cerebral cortex are affected. GRN mutation cases are quantitatively different from sporadic cases, while cases with associated HS and AD have increased densities of dystrophic neurites and abnormally enlarged neurones respectively. There is little correlation between the subjective assessment of subtypes and the more objective quantitative data.
Review: The architecture of inflammatory demyelinating lesions: implications for studies on pathogenesis
Authors: Lassmann H. 
Published: June 2011

H. Lassmann (2011) Neuropathology and Applied Neurobiology37, 698–710The architecture of inflammatory demyelinating lesions: implications for studies on pathogenesisRecent technological advances provided the chance to analyse the molecular events involved in the pathogenesis of lesions in human disease. A major prerequisite for such studies is, however, that the pathological material used is exactly defined and characterized. In multiple sclerosis (MS), this is difficult, as several types of active lesions exist, depending upon the stage of the disease, the age and location of these lesions and the inter‐individual differences between patients. In addition, within an active lesion, different closely adjacent zones are present reflecting initial tissue injury, debris removal or repair. Here evidence is reviewed, showing that distinct subareas of active MS lesions reflect different pathological hallmarks of lesion evolution. These data provide the basis for our understanding of the pathogenesis of tissue injury in MS and imply that studies on MS pathogenesis have to rely on a clear definition of the lesions analysed and have to focus on specific lesion areas, isolated by microdissection. In addition, these data also imply that molecules, identified in these studies, must be confirmed and validated in the correct context of lesion initiation and/or progression.
BRAF‐KIAA1549 fusion transcripts are less frequent in pilocytic astrocytomas diagnosed in adults
Authors: Hasselblatt M. , Riesmeier B. , Lechtape B. , Brentrup A. , Stummer W. , Albert F. K. , Sepehrnia A. , Ebel H. , Gerß J. , Paulus W. 
Published: June 2011

M. Hasselblatt, B. Riesmeier, B. Lechtape, A. Brentrup, W. Stummer, F. K. Albert, A. Sepehrnia, H. Ebel, J. Gerß and W. Paulus (2011) Neuropathology and Applied Neurobiology37, 803–806BRAF‐KIAA1549 fusion transcripts are less frequent in pilocytic astrocytomas diagnosed in adultsAim: Duplication of 7q34 resulting in generation of BRAF‐KIAA1549 fusion transcripts is a characteristic event in pilocytic astrocytoma that may also aid distinction from diffuse astrocytic tumours. As data on BRAF‐KIAA1549 fusion transcript status remain mainly limited to children, we aimed to examine the diagnostic value of BRAF‐KIAA1549 fusion transcripts across all age groups. Methods:BRAF‐KIAA1549 fusion transcript status was examined using reverse transcription polymerase chain reaction on formalin‐fixed paraffin‐embedded samples of 105 primary pilocytic astrocytomas [median patient age: 17 years (1–74 years)]. Results: Informative results (distinct wildtype BRAF bands detectable) were obtained in 105/124 cases (85%). Fusion transcripts were detected in 53 of cases (51%). They were more often encountered in tumours of infratentorial location [42/67 (63%) vs. 11/38 (29%)] and comprised KIAA1549‐Ex16_BRAF‐Ex9 (32 cases), KIAA1549‐Ex15_BRAF‐Ex9 (14 cases) and KIAA1549‐Ex16_BRAF‐Ex11 (seven cases). Fusion transcripts were present in 79% of tumours diagnosed in the first decade of life, but only in 51% of patients aged 11–20 years, 42% of patients aged 21–30 years, 30% of patients aged 31–40 years and 7% of patients older than 40 years. On multivariate logistic regression analysis, the association of fusion transcript status and age was confirmed adjusting for tumour location (P = 0.006). Conclusions: The frequency of BRAF‐KIAA1549 fusion transcripts is significantly lower in adult patients with pilocytic astrocytoma, weakening the sensitivity of this specific diagnostic marker in that age group.
Unmyelinated axons are more vulnerable to degeneration than myelinated axons of the cardiac nerve in Parkinson's disease
Authors: Orimo S. , Uchihara T. , Kanazawa T. , Itoh Y. , Wakabayashi K. , Kakita A. , Takahashi H. 
Published: June 2011

S. Orimo, T. Uchihara, T. Kanazawa, Y. Itoh, K. Wakabayashi, A. Kakita and H. Takahashi (2011) Neuropathology and Applied Neurobiology37, 791–802Unmyelinated axons are more vulnerable to degeneration than myelinated axons of the cardiac nerve in Parkinson's diseaseAims: We recently demonstrated accumulation of α‐synuclein aggregates of the cardiac sympathetic nerve in Parkinson's disease (PD) and a possible relationship between degeneration of the cardiac sympathetic nerve and α‐synuclein aggregates. The aim of this study is to determine whether there is a difference in the degenerative process between unmyelinated and myelinated axons of the cardiac nerve. Methods: We immunohistochemically examined cardiac tissues from four pathologically verified PD patients, nine patients with incidental Lewy body disease (ILBD) and five control subjects, using antibodies against neurofilament, myelin basic protein (MBP) and α‐synuclein. First, we counted the number of neurofilament‐immunoreactive axons not surrounded by MBP (unmyelinated axons) and those surrounded by MBP (myelinated axons). Next, we counted the number of unmyelinated and myelinated axons with α‐synuclein aggregates. Results: (i) The percentage of unmyelinated axons in PD (77.5 ± 9.14%) was significantly lower compared to that in control subjects (92.2 ± 2.40%). (ii) The ratio of unmyelinated axons with α‐synuclein aggregates to total axons with α‐synuclein aggregates in ILBD ranged from 94.4 to 100 (98.2 ± 2.18%). Among axons with α‐synuclein aggregates, unmyelinated axons were the overwhelming majority, comprising 98.2%. Conclusion: These findings suggest that in PD unmyelinated axons are more vulnerable to degeneration than myelinated axons of the cardiac nerve, because α‐synuclein aggregates accumulate much more abundantly in unmyelinated axons.
Septic metastatic encephalitis: coexistence of brain damage and repair
Authors: Tauber S. C. , Bunkowski S. , Brück W. , Nau R. 
Published: June 2011

S. C. Tauber, S. Bunkowski, W. Brück and R. Nau (2011) Neuropathology and Applied Neurobiology37, 768–776Septic metastatic encephalitis: coexistence of brain damage and repairAims: Septic metastatic encephalitis (SME) arises from systemic bacterial infections and is a severe complication of sepsis with a high mortality. In this study, we examined the neuropathological findings in humans suffering from SME including white matter pathology and proliferation of neural precursor cells in the hippocampal dentate gyrus. Methods: The brains of 10 autopsy cases with SME and 10 control cases after sudden death from non‐neurological causes were studied by means of immunohistochemistry. Results: We found diffuse axonal injury and demyelination in the frontal cortex (P = 0.01) as well as increased numbers of recently generated TUC‐4 expressing neurones in the hippocampal dentate gyrus in SME cases (P = 0.01). The median density of apoptotic granule cells in the dentate gyrus also was higher in SME cases, the difference, however, failed to reach statistical significance (P = 0.25). Conclusion: The coexistence of degenerative processes predominantly in the neocortex and regenerative activity in the hippocampal formation known from bacterial meningitis also characterizes the pathology of SME.