Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus.


BACKGROUND:Several in vitro studies document the function of the transcriptional regulator TrmBL1 of Pyrococcus furiosus. These data indicate that the protein can act as repressor or activator and is mainly involved in transcriptional control of sugar uptake and in the switch between glycolysis and gluconeogenesis. The aim of this study was to complement the in vitro data with an in vivo analysis using ChIP-seq to explore the genome-wide binding profile of TrmBL1 under glycolytic and gluconeogenic growth conditions. RESULTS:The ChIP-seq analysis revealed under gluconeogenic growth conditions 28 TrmBL1 binding sites where the TGM is located upstream of coding regions and no binding sites under glycolytic conditions. The experimental confirmation of the binding sites using qPCR, EMSA, DNase I footprinting and in vitro transcription experiments validated the in vivo identified TrmBL1 binding sites. Furthermore, this study provides evidence that TrmBL1 is also involved in transcriptional regulation of additional cellular processes e.g. amino acid metabolism, transcriptional control or metabolic pathways. In the initial setup we were interested to include the binding analysis of TrmB, an additional member of the TrmB family, but western blot experiments and the ChIP-seq data indicated that the corresponding gene is deleted in our Pyrococcus strain. A detailed analysis of a new type strain demonstrated that a 16 kb fragment containing the trmb gene is almost completely deleted after the first re-cultivation. CONCLUSIONS:The identified binding sites in the P. furiosus genome classified TrmBL1 as a more global regulator as hitherto known. Furthermore, the high resolution of the mapped binding positions enabled reliable predictions, if TrmBL1 activates (binding site upstream of the promoter) or represses transcription (binding site downstream) of the corresponding genes.


BMC Genomics


BMC genomics


Reichelt R,Gindner A,Thomm M,Hausner W




Has Abstract


2016-01-08 00:00:00










  • Are personalities genetically determined? Inferences from subsocial spiders.

    abstract:BACKGROUND:Recent research has revealed that polymorphic behavioral strategies shape intra-and interspecific interactions and contribute to fitness in many animal species. A better understanding of the proximate mechanisms underlying these behavioral syndromes will enhance our grasp this phenomenon. Spiders in the genu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Purcell J,Pruitt JN

    更新日期:2019-11-22 00:00:00

  • Genome-wide metabolic (re-) annotation of Kluyveromyces lactis.

    abstract:BACKGROUND:Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic anal...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dias O,Gombert AK,Ferreira EC,Rocha I

    更新日期:2012-10-01 00:00:00

  • Identification of sensory hair-cell transcripts by thiouracil-tagging in zebrafish.

    abstract:BACKGROUND:Sensory hair cells are exquisitely sensitive to mechanical stimuli and as such, are prone to damage and apoptosis during dissections or in vitro manipulations. Thiouracil (TU)-tagging is a noninvasive method to label cell type-specific transcripts in an intact organism, thereby meeting the challenge of how t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Erickson T,Nicolson T

    更新日期:2015-10-23 00:00:00

  • Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle.

    abstract:BACKGROUND:Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid sub...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li X,Ma Y,Liang S,Tian Y,Yin S,Xie S,Xie H

    更新日期:2018-12-07 00:00:00

  • Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).

    abstract:BACKGROUND:Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding program...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Houston RD,Taggart JB,Cézard T,Bekaert M,Lowe NR,Downing A,Talbot R,Bishop SC,Archibald AL,Bron JE,Penman DJ,Davassi A,Brew F,Tinch AE,Gharbi K,Hamilton A

    更新日期:2014-02-06 00:00:00

  • Gene2vec: distributed representation of genes based on co-expression.

    abstract:BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Du J,Jia P,Dai Y,Tao C,Zhao Z,Zhi D

    更新日期:2019-02-04 00:00:00

  • Prediction of enhancer-promoter interactions via natural language processing.

    abstract:BACKGROUND:Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting o...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zeng W,Wu M,Jiang R

    更新日期:2018-05-09 00:00:00

  • Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium.

    abstract:BACKGROUND:Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu S,Tang S,Tan Z,Yu Y,Dai Q,Liu T

    更新日期:2017-01-10 00:00:00

  • Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium.

    abstract:BACKGROUND:The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. There has been little invest...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Frangeul L,Quillardet P,Castets AM,Humbert JF,Matthijs HC,Cortez D,Tolonen A,Zhang CC,Gribaldo S,Kehr JC,Zilliges Y,Ziemert N,Becker S,Talla E,Latifi A,Billault A,Lepelletier A,Dittmann E,Bouchier C,de Marsac NT

    更新日期:2008-06-05 00:00:00

  • ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.

    abstract:BACKGROUND:Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such fac...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Davenport ER,Goodrich JK,Bell JT,Spector TD,Ley RE,Clark AG

    更新日期:2016-11-21 00:00:00

  • High-throughput comparison of gene fitness among related bacteria.

    abstract:BACKGROUND:The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Canals R,Xia XQ,Fronick C,Clifton SW,Ahmer BM,Andrews-Polymenis HL,Porwollik S,McClelland M

    更新日期:2012-05-30 00:00:00

  • Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni.

    abstract:BACKGROUND:It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Laha T,Kewgrai N,Loukas A,Brindley PJ

    更新日期:2005-11-04 00:00:00

  • atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

    abstract:BACKGROUND:Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. A...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ding Y,Chen M,Liu Z,Ding D,Ye Y,Zhang M,Kelly R,Guo L,Su Z,Harris SC,Qian F,Ge W,Fang H,Xu X,Tong W

    更新日期:2012-07-20 00:00:00

  • High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation.

    abstract:BACKGROUND:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey o...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bi YM,Meyer A,Downs GS,Shi X,El-Kereamy A,Lukens L,Rothstein SJ

    更新日期:2014-01-28 00:00:00

  • Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae.

    abstract:BACKGROUND:Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS:This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, us...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jin L,Li G,Yu D,Huang W,Cheng C,Liao S,Wu Q,Zhang Y

    更新日期:2017-02-06 00:00:00

  • SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.

    abstract:BACKGROUND:The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. RESULTS:Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment)...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Agostini F,Cirillo D,Ponti RD,Tartaglia GG

    更新日期:2014-10-23 00:00:00

  • A Caenorhabditis motif compendium for studying transcriptional gene regulation.

    abstract:BACKGROUND:Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dieterich C,Sommer RJ

    更新日期:2008-01-23 00:00:00

  • Genome-wide transcriptional analysis of T cell activation reveals differential gene expression associated with psoriasis.

    abstract:BACKGROUND:Psoriasis is a chronic autoimmune disease in which T cells have a predominant role in initiating and perpetuating the chronic inflammation in skin. However, the mechanisms that regulate T cell activation in psoriasis are still incompletely understood. The objective of the present study was to characterize th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Palau N,Julià A,Ferrándiz C,Puig L,Fonseca E,Fernández E,López-Lasanta M,Tortosa R,Marsal S

    更新日期:2013-11-23 00:00:00

  • Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands.

    abstract:BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma L,Ma Q,Li X,Cheng L,Li K,Li S

    更新日期:2014-03-09 00:00:00

  • Bcheck: a wrapper tool for detecting RNase P RNA genes.

    abstract:BACKGROUND:Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily spec...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yusuf D,Marz M,Stadler PF,Hofacker IL

    更新日期:2010-07-13 00:00:00

  • Specificity and overlap in gene segment-defined antibody repertoires.

    abstract:BACKGROUND:To date several studies have sought to catalog the full suite of antibodies that humans naturally produce against single antigens or other specificities (repertoire). Here we analyze the properties of all sequenced repertoires in order to better understand the specificity of antibody responses. Specifically,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Arnaout RA

    更新日期:2005-10-28 00:00:00

  • Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows.

    abstract:BACKGROUND:The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ov...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sun X,Mei S,Tao H,Wang G,Su L,Jiang S,Deng C,Xiong Y,Li F

    更新日期:2011-02-16 00:00:00

  • Genome sequence of an aflatoxigenic pathogen of Argentinian peanut, Aspergillus arachidicola.

    abstract:BACKGROUND:Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Moore GG,Mack BM,Beltz SB,Puel O

    更新日期:2018-03-09 00:00:00

  • Estimating the total genome length of a metagenomic sample using k-mers.

    abstract:BACKGROUND:Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hua K,Zhang X

    更新日期:2019-04-04 00:00:00

  • Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents.

    abstract:BACKGROUND:Protein and mRNA levels for several selenoproteins, such as glutathione peroxidase-1 (Gpx1), are down-regulated dramatically by selenium (Se) deficiency. These levels in rats increase sigmoidally with increasing dietary Se and reach defined plateaus at the Se requirement, making them sensitive biomarkers for...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Raines AM,Sunde RA

    更新日期:2011-01-12 00:00:00

  • Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis).

    abstract:BACKGROUND:Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looke...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang JZ,Zhao K,Ai XY,Hu CG

    更新日期:2014-10-13 00:00:00

  • Systems toxicology identifies mechanistic impacts of 2-amino-4,6-dinitrotoluene (2A-DNT) exposure in Northern Bobwhite.

    abstract:BACKGROUND:A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to develop holistic effects characterizations for the wildlife bird model, Northern bobwhite (Colinus virginianus) dosed with the explosives degradation product 2-amino-4,6-dinitrotoluene (2A-DNT)....

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gust KA,Nanduri B,Rawat A,Wilbanks MS,Ang CY,Johnson DR,Pendarvis K,Chen X,Quinn MJ Jr,Johnson MS,Burgess SC,Perkins EJ

    更新日期:2015-08-07 00:00:00

  • Coevolution of paired receptors in Xenopus carcinoembryonic antigen-related cell adhesion molecule families suggests appropriation as pathogen receptors.

    abstract:BACKGROUND:In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zimmermann W,Kammerer R

    更新日期:2016-11-16 00:00:00

  • Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice.

    abstract:BACKGROUND:Lung aging is characterized by a number of structural alterations including fibrosis, chronic inflammation and the alteration of inflammatory cell composition. Chronic exposure to cigarette smoke (CS) is known to induce similar alterations and may contribute to premature lung aging. Additionally, aging and C...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Choukrallah MA,Hoeng J,Peitsch MC,Martin F

    更新日期:2020-04-09 00:00:00

  • GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane.

    abstract:BACKGROUND:Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Balsalobre TW,da Silva Pereira G,Margarido GR,Gazaffi R,Barreto FZ,Anoni CO,Cardoso-Silva CB,Costa EA,Mancini MC,Hoffmann HP,de Souza AP,Garcia AA,Carneiro MS

    更新日期:2017-01-11 00:00:00