Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis.

Abstract:

:In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase "core enzyme" (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the σ(S)-associated RNA polymerase form (Eσ(S)) during transition from exponential to stationary phase. We identified 63 binding sites for Eσ(S) overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the σ(S)-encoding rpoS gene. Eσ(S) binding did not always correlate with an increase in transcription level, suggesting that, at some σ(S)-dependent promoters, Eσ(S) might remain poised in a pre-initiation state upon binding. A large fraction of Eσ(S)-binding sites corresponded to promoters recognized by RNA polymerase associated with σ(70) or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, Eσ(S) appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of Eσ(S) in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Peano C,Wolf J,Demol J,Rossi E,Petiti L,De Bellis G,Geiselmann J,Egli T,Lacour S,Landini P

doi

10.1038/srep10469

subject

Has Abstract

pub_date

2015-05-28 00:00:00

pages

10469

issn

2045-2322

pii

srep10469

journal_volume

5

pub_type

杂志文章
  • Complex inheritance in Pulmonary Arterial Hypertension patients with several mutations.

    abstract::Pulmonary Arterial Hypertension (PAH) is a rare and progressive disease with low incidence and prevalence, and elevated mortality. PAH is characterized by increased mean pulmonary artery pressure. The aim of this study was to analyse patients with combined mutations in BMPR2, ACVRL1, ENG and KCNA5 genes and to establi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep33570

    authors: Pousada G,Baloira A,Valverde D

    更新日期:2016-09-15 00:00:00

  • Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate.

    abstract::It is recently appreciated that many bacterial chemoreceptors have ligand-binding domains (LBD) of the dCACHE family, a structure with two PAS-like subdomains, one membrane-proximal and the other membrane-distal. Previous studies had implicated only the membrane-distal subdomain in ligand recognition. Here, we report ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14372-2

    authors: Machuca MA,Johnson KS,Liu YC,Steer DL,Ottemann KM,Roujeinikova A

    更新日期:2017-10-26 00:00:00

  • Pharmacological targeting of glucose-6-phosphate dehydrogenase in human erythrocytes by Bay 11-7082, parthenolide and dimethyl fumarate.

    abstract::In mature erythrocytes, glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) yield NADPH, a crucial cofactor of the enzyme glutathione reductase (GR) converting glutathione disulfide (GSSG) into its reduced state (GSH). GSH is essential for detoxification processes in and survival of ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep28754

    authors: Ghashghaeinia M,Giustarini D,Koralkova P,Köberle M,Alzoubi K,Bissinger R,Hosseinzadeh Z,Dreischer P,Bernhardt I,Lang F,Toulany M,Wieder T,Mojzikova R,Rossi R,Mrowietz U

    更新日期:2016-06-29 00:00:00

  • Identification and Structural Characterization of the N-terminal Amyloid Core of Orb2 isoform A.

    abstract::Orb2 is a functional amyloid that plays a key role in Drosophila long-term memory formation. Orb2 has two isoforms that differ in their N-termini. The N-terminus of the A isoform (Orb2A) that precedes its Q-rich prion-like domain has been shown to be important for Orb2 aggregation and long-term memory. However, beside...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38265

    authors: Cervantes SA,Bajakian TH,Soria MA,Falk AS,Service RJ,Langen R,Siemer AB

    更新日期:2016-12-06 00:00:00

  • Carbonated rankinite binder: effect of curing parameters on microstructure, strength development and durability performance.

    abstract::Due to the high CO2-footprint of ordinary Portland cement (OPC), the search for alternative binders is now in a full swing. Rankinite-which is a hydraulically inactive material and low in calcium, is a real alternative to OPC, as it absorbs the harmful greenhouse gas from the air through carbonation hardening. Neverth...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-71270-w

    authors: Smigelskyte A,Siauciunas R,Hilbig H,Decker M,Urbonas L,Skripkiunas G

    更新日期:2020-09-02 00:00:00

  • Lipid Droplet-Associated Hydrolase Promotes Lipid Droplet Fusion and Enhances ATGL Degradation and Triglyceride Accumulation.

    abstract::Lipid droplet (LD)-associated hydrolase (LDAH) is a newly identified LD protein abundantly expressed in tissues that predominantly store triacylglycerol (TAG). However, how LDAH regulates TAG metabolism remains unknown. We found that upon oleic acid loading LDAH translocalizes from the ER to newly formed LDs, and indu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02963-y

    authors: Goo YH,Son SH,Paul A

    更新日期:2017-06-02 00:00:00

  • A new marine-derived sulfoglycolipid triggers dendritic cell activation and immune adjuvant response.

    abstract::Dendritic Cells (DCs) recognize infectious non-self molecules and engage the adaptive immune system thereby initiating long lasting, antigen-specific responses. As such, the ability to activate DCs is considered a key tool to enhance the efficacy and quality of vaccination. Here we report a novel immunomodulatory sulf...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05969-8

    authors: Manzo E,Cutignano A,Pagano D,Gallo C,Barra G,Nuzzo G,Sansone C,Ianora A,Urbanek K,Fenoglio D,Ferrera F,Bernardi C,Parodi A,Pasquale G,Leonardi A,Filaci G,De Palma R,Fontana A

    更新日期:2017-07-24 00:00:00

  • Effect of Substrate Surface Roughening on the Capacitance and Cycling Stability of Ni(OH)2 Nanoarray Films.

    abstract::The effect of substrate surface roughening on the capacitance of Ni(OH)2/NiOOH nanowall array samples produced via chemical bath deposition for 2, 4, 6, 24 and 48 h on an as-received stainless steel substrate and the same substrate after sandblasting has been investigated. Symmetric cells were subjected to 120,000 cha...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-53365-1

    authors: Pimsawat A,Tangtrakarn A,Pimsawat N,Daengsakul S

    更新日期:2019-11-14 00:00:00

  • Multi-frequency complex network from time series for uncovering oil-water flow structure.

    abstract::Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncove...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08222

    authors: Gao ZK,Yang YX,Fang PC,Jin ND,Xia CY,Hu LD

    更新日期:2015-02-04 00:00:00

  • The influence of four pharmaceuticals on Chlorellapyrenoidosa culture.

    abstract::There has been a developing technology in algae with pharmaceuticals wastewater. However, the effect and the underlying mechanism of pharmaceuticals on algae are not well understood. To investigate the effect and mechanism of pharmaceuticalson microalgae, four pharmaceuticals of clofibric acid (CLF), ciprofloxacin (CI...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-36609-4

    authors: Zhang Y,Guo J,Yao T,Zhang Y,Zhou X,Chu H

    更新日期:2019-02-07 00:00:00

  • The strange flight behaviour of slowly spinning soccer balls.

    abstract::The strange three-dimensional flight behaviour of slowly spinning soccer balls is one of the most interesting and unknown phenomenon associated with the trajectories of sports balls. Many spectators have experienced numerous exciting and emotional instances while observing the curious flight behaviour of these balls. ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep01871

    authors: Mizota T,Kurogi K,Ohya Y,Okajima A,Naruo T,Kawamura Y

    更新日期:2013-01-01 00:00:00

  • Effect of aspect ratio and surface defects on the photocatalytic activity of ZnO nanorods.

    abstract::ZnO, aside from TiO2, has been considered as a promising material for purification and disinfection of water and air, and remediation of hazardous waste, owing to its high activity, environment-friendly feature and lower cost. However, their poor visible light utilization greatly limited their practical applications. ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep04596

    authors: Zhang X,Qin J,Xue Y,Yu P,Zhang B,Wang L,Liu R

    更新日期:2014-04-04 00:00:00

  • Role of HIV exposure and infection in relation to neonatal GBS disease and rectovaginal GBS carriage: a systematic review and meta-analysis.

    abstract::Streptococcus agalactiae (GBS) is the leading cause worldwide of neonatal sepsis. We sought to assess to which extent HIV exposure of neonates is associated with GBS neonatal disease. Furthermore, we assessed to which extent HIV infection in women is associated with maternal rectovaginal GBS carriage, the single most ...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析

    doi:10.1038/s41598-017-13218-1

    authors: Cools P,van de Wijgert JHHM,Jespers V,Crucitti T,Sanders EJ,Verstraelen H,Vaneechoutte M

    更新日期:2017-10-23 00:00:00

  • Current controlled switching of impedance in magnetic conductor with tilted anisotropy easy axis and its applications.

    abstract::We present a concept and prototype of a memory element based on current driven magneto-impedance (MI) effect that stores the binary data (0, 1) as the orientation of the magnetization. The magnetization orientation in the surface layer with tilted anisotropy easy axis can be switched controllably between two stable st...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36180

    authors: Ipatov M,Zhukova V,Zhukov A,Gonzalez J

    更新日期:2016-10-26 00:00:00

  • Three tandem promoters, together with IHF, regulate growth phase dependent expression of the Escherichia coli kps capsule gene cluster.

    abstract::In this study we characterise three tandem promoters (PR1-1, PR1-2 and PR1-3) within the PR1 regulatory region of the Escherichia coli kps capsule gene cluster. Transcription from promoter PR1-2 was dependent on the activity of the upstream promoter PR1-1, which activated PR1-2 via transcription coupled DNA supercoili...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17891-0

    authors: Jia J,King JE,Goldrick MC,Aldawood E,Roberts IS

    更新日期:2017-12-20 00:00:00

  • Direct Band Gap Gallium Antimony Phosphide (GaSbxP(1-x)) Alloys.

    abstract::Here, we report direct band gap transition for Gallium Phosphide (GaP) when alloyed with just 1-2 at% antimony (Sb) utilizing both density functional theory based computations and experiments. First principles density functional theory calculations of GaSbxP(1-x) alloys in a 216 atom supercell configuration indicate t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20822

    authors: Russell HB,Andriotis AN,Menon M,Jasinski JB,Martinez-Garcia A,Sunkara MK

    更新日期:2016-02-10 00:00:00

  • Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study.

    abstract::Technical advances including liquid chromatography-tandem mass spectrometry and its data analysis enable detailed proteomic analysis of the nasal mucus. Alterations of the nasal mucus proteome may provoke substantial changes of the nasal physiology and have already been associated with rhinologic diseases such as alle...

    journal_title:Scientific reports

    pub_type: 临床试验,杂志文章

    doi:10.1038/s41598-018-35776-8

    authors: Wolf A,Liesinger L,Spoerk S,Schittmayer M,Lang-Loidolt D,Birner-Gruenberger R,Tomazic PV

    更新日期:2018-12-03 00:00:00

  • Black P/graphene hybrid: A fast response humidity sensor with good reversibility and stability.

    abstract::Black phosphorus (BP) materials have attracted considerable attention owing to their ultra-sensitive humidity sensing characteristics because of the natural absorption of water (H2O) molecules on the BP surface caused by the specific 2D layer-crystalline structure. On the other hand, the BP-based humidity sensor is le...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10848-3

    authors: Phan DT,Park I,Park AR,Park CM,Jeon KJ

    更新日期:2017-09-05 00:00:00

  • CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer.

    abstract::Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent post-transcriptional modification of RNA molecules. Researchers have attempted to find reliable RNA editing using next generation sequencing (NGS) data. However, most of these attempts suffered from a high rate of false positives, and they did not conside...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-41294-y

    authors: Hwang W,Calza S,Silvestri M,Pawitan Y,Lee Y

    更新日期:2019-03-25 00:00:00

  • The linear artifact in enhanced depth imaging spectral domain optical coherence tomography.

    abstract::Optical coherence tomography (OCT) is a valuable ancillary test in the diagnosis and management of chorioretinal disease. The evaluation of choroid thickness using OCT has become the focus of clinical applications. We report a linear artifact that acts as a confounding factor in choroidal thickness measurements by enh...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08811-3

    authors: Zuo C,Mi L,Yang S,Guo X,Xiao H,Liu X

    更新日期:2017-08-16 00:00:00

  • The potential of incorporation of binary salts and ionic liquid in P(VP-co-VAc) gel polymer electrolyte in electrochemical and photovoltaic performances.

    abstract::In this study, dye-sensitized solar cells (DSSCs) has been assembled with poly(1-vinylpyrrolidone-co-vinyl acetate) (P(VP-co-VAc)) gel polymer electrolytes (GPEs) which have been incorporated with binary salt and an ionic liquid. The potential of this combination was studied and reported. The binary salt system GPEs w...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep27630

    authors: Ming NH,Ramesh S,Ramesh K

    更新日期:2016-06-08 00:00:00

  • Interactive machine learning for soybean seed and seedling quality classification.

    abstract::New computer vision solutions combined with artificial intelligence algorithms can help recognize patterns in biological images, reducing subjectivity and optimizing the analysis process. The aim of this study was to propose an approach based on interactive and traditional machine learning methods to classify soybean ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-68273-y

    authors: de Medeiros AD,Capobiango NP,da Silva JM,da Silva LJ,da Silva CB,Dos Santos Dias DCF

    更新日期:2020-07-09 00:00:00

  • Automatic release of silicon nanowire arrays with a high integrity for flexible electronic devices.

    abstract::Automatic release and vertical transferring of silicon/silicon oxide nanowire arrays with a high integrity are demonstrated by an Ag-assisted ammonia etching method. By adding a water steaming step between Ag-assisted HF/H2O2 and ammonia etching to form a SiOx protective layer sheathing Si nanowires, we can tune the c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep03940

    authors: Wu L,Li S,He W,Teng D,Wang K,Ye C

    更新日期:2014-02-03 00:00:00

  • Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.

    abstract::Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-20889-x

    authors: Wilkinson DA,O'Donnell AJ,Akhter RN,Fayaz A,Mack HJ,Rogers LE,Biggs PJ,French NP,Midwinter AC

    更新日期:2018-02-05 00:00:00

  • Publisher Correction: Emergence of Different Recombinant Porcine Reproductive and Respiratory Syndrome Viruses, China.

    abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-018-25625-z

    authors: Liu Y,Li J,Yang J,Zeng H,Guo L,Ren S,Sun W,Chen Z,Cong X,Shi J,Chen L,Du Y,Li J,Wang J,Wu J,Yu J

    更新日期:2018-05-23 00:00:00

  • Quantum state transfer via Bloch oscillations.

    abstract::The realization of reliable quantum channels, able to transfer a quantum state with high fidelity, is a fundamental step in the construction of scalable quantum devices. In this paper we describe a transmission scheme based on the genuinely quantum effect known as Bloch oscillations. The proposed protocol makes it pos...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep26054

    authors: Tamascelli D,Olivares S,Rossotti S,Osellame R,Paris MG

    更新日期:2016-05-18 00:00:00

  • Hyperuricemia and overexcretion of uric acid increase the risk of simple renal cysts in type 2 diabetes.

    abstract::Previous studies have discussed the relationship between simple renal cysts (SRC) and serum uric acid level in healthy individuals. We performed a cross-sectional study to evaluate the association between serum uric acid level and fractional excretion of uric acid (FEUA) and simple renal cysts in males and postmenopau...

    journal_title:Scientific reports

    pub_type: 临床试验,杂志文章

    doi:10.1038/s41598-017-04036-6

    authors: Han Y,Zhang M,Lu J,Zhang L,Han J,Zhao F,Chen H,Bao Y,Jia W

    更新日期:2017-06-19 00:00:00

  • Comparison study between mesoporous silica nanoscale microsphere and active carbon used as the matrix of shape-stabilized phase change material.

    abstract::Mesoporous silica nanoscale microsphere (MSNM), with a special morphology, high porosity, large pore volume and specific surface area, was successfully prepared and used as the matrix material of lauric acid (LA) to prepare a favorable shape-stabilized phase change material (LA/MSNM). The porous network structure of M...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-52553-3

    authors: Zhang Z,Wang J,Tang X,Liu Y,Han Z,Chen Y

    更新日期:2019-11-05 00:00:00

  • Vertical-type two-dimensional hole gas diamond metal oxide semiconductor field-effect transistors.

    abstract::Power semiconductor devices require low on-resistivity and high breakdown voltages simultaneously. Vertical-type metal-oxide-semiconductor field-effect transistors (MOSFETs) meet these requirements, but have been incompleteness in diamond. Here we show vertical-type p-channel diamond MOSFETs with trench structures and...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28837-5

    authors: Oi N,Inaba M,Okubo S,Tsuyuzaki I,Kageura T,Onoda S,Hiraiwa A,Kawarada H

    更新日期:2018-07-13 00:00:00

  • The crystal structure of the Sgt1-Skp1 complex: the link between Hsp90 and both SCF E3 ubiquitin ligases and kinetochores.

    abstract::The essential cochaperone Sgt1 recruits Hsp90 chaperone activity to a range of cellular factors including SCF E3 ubiquitin ligases and the kinetochore in eukaryotes. In these pathways Sgt1 interacts with Skp1, a small protein that heterodimerizes with proteins containing the F-box motif. We have determined the crystal...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41626

    authors: Willhoft O,Kerr R,Patel D,Zhang W,Al-Jassar C,Daviter T,Millson SH,Thalassinos K,Vaughan CK

    更新日期:2017-01-31 00:00:00