Publications

Abstract (Expand)

A quantitative proteomic analysis of the membrane of the archaeon Sulfolobus solfataricus P2 using iTRAQ was successfully demonstrated in this technical note. The estimated number of membrane proteins ...

Authors: None

Date Published: 4th Dec 2009

Journal: J. Proteome Res.

Abstract (Expand)

A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to ...

Authors: Kenneth Timmis, Vitor Martins Dos Santos, Puchałka Jacek,Oberhardt Matthew A,Godinho Miguel,Bielecka Agata,Regenhardt Daniela,Papin Jason A

Date Published: 27th Mar 2008

Journal: PLoS Comput. Biol.

Abstract (Expand)

Pseudomonas putida DOT-T1E is a highly solvent-tolerant strain. Although the main mechanism that confers solvent tolerance to the strain is the TtgGHI efflux pump, a number of other proteins are also ...

Authors: Juan Ramos, García Vanina,Godoy Patricia,Daniels Craig,Hurtado Ana,Segura Ana

Date Published: 1st Nov 2009

Journal: Not specified

Abstract (Expand)

Pseudomonas putida is a soil microorganism that utilizes aromatic amino acids present in root exudates as a nitrogen source. We have previously shown that the PhhR transcriptional regulator induces ...

Authors: Estrella Duque, Juan Ramos, Herrera M. Carmen,Rodríguez-Herva José J.,Fernández-Escamilla Ana M.

Date Published: 2010

Journal: Not specified

Abstract (Expand)

Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we ...

Authors: M. Tauqeer Alam, Maria Elena Merlo, David Hodgson, Elizabeth Wellington, Eriko Takano, Rainer Breitling, (stream) The STREAM Consortium

Date Published: 2010

Journal: BMC Genomics

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BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene ...

Authors: Kay Nieselt, Per Bruheim, Alexander Wentzel, Øyvind Jakobsen, Håvard Sletta, M. Tauqeer Alam, Maria Elena Merlo, Jay Moore, Walid Omara, Antonio Rodríguez-García, Louise Thomas, Roxane Legaie, William Gaze, Gregory Challis, R Jansen, Lubbert Dijkhuizen, David Rand, David Wild, Jens Reuther, Wolfgang Wohlleben, Maggie Smith, Nigel Burroughs, Juan-Francisco Martin, David Hodgson, Eriko Takano, Rainer Breitling, Trond Ellingsen, Elizabeth Wellington, Battke Florian,Herbig Alexander,Morrissey Edward R,Juarez-Hermosillo Miguel A,Nentwich Merle,Iqbal Mudassar,Bonin Michael

Date Published: 28th May 2009

Journal: BMC Genomics

Abstract (Expand)

Many microorganisms, including bacteria of the class Streptomycetes, produce various secondary metabolites including antibiotics to gain a competitive advantage in their natural habitat. The production ...

Authors: Eriko Takano, Mehra Sarika,Charaniya Salim,Hu Wei-Shou

Date Published: 2nd May 2008

Journal: PLoS ONE

Abstract (Expand)

Antibiotic production is regulated by numerous signals, including the so-called bacterial hormones found in antibiotic producing organisms such as Streptomyces. These signals, the gamma-butyrolactones, ...

Authors: Eriko Takano, Hsiao Nai-Hua,Gottelt Marco

Date Published: 21st Apr 2009

Journal: Meth. Enzymol.

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The computational reconstruction and analysis of cellular models of microbial metabolism is one of the great success stories of systems biology. The extent and quality of metabolic network reconstructions ...

Authors: Rainer Breitling, Vitkup Dennis,Barrett Michael P

Date Published: 21st Nov 2007

Journal: Nat. Rev. Microbiol.

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SUMMARY: We present a Cytoscape plugin for the inference and visualization of networks from high-resolution mass spectrometry metabolomic data. The software also provides access to basic topological ...

Authors: Rainer Breitling, Jourdan Fabien,Barrett Michael P,Gilbert David

Date Published: 14th Nov 2007

Journal: Bioinformatics

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MOTIVATION: High-accuracy mass spectrometry is a popular technology for high-throughput measurements of cellular metabolites (metabolomics). One of the major challenges is the correct identification ...

Authors: Rainer Breitling, Rogers Simon,Scheltema Richard A,Girolami Mark

Date Published: 18th Dec 2008

Journal: Bioinformatics

Abstract (Expand)

With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel computational ...

Authors: R Jansen, Rainer Breitling, Scheltema Richard A,Kamleh Anas,Wildridge David,Ebikeme Charles,Watson David G,Barrett Michael P

Date Published: 22nd Oct 2008

Journal: Proteomics

Abstract (Expand)

The transport of inorganic phosphate (P(i)) is essential for the growth of all organisms. The metabolism of soil-dwelling Streptomyces species, and their ability to produce antibiotics and other secondary ...

Authors: Antonio Rodríguez-García, Juan-Francisco Martin, Santos-Beneit Fernando,Franco-Domínguez Etelvina

Date Published: 1st Aug 2008

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

Bacterial growth requires equilibrated concentration of C, N and P sources. This work shows a phosphate control over the nitrogen metabolism in the model actinomycete Streptomyces coelicolor. Phosphate ...

Authors: Antonio Rodríguez-García, Juan-Francisco Martin, Sola-Landa Alberto,Apel Kristian,Santos-Beneit Fernando

Date Published: 24th Mar 2009

Journal: Nucleic Acids Res.

Abstract (Expand)

Mycobacterium tuberculosis can utilize various nutrients including nitrate as a source of nitrogen. Assimilation of nitrate requires the reduction of nitrate via nitrite to ammonium, which is then ...

Authors: Frank Schmidt, Wolfgang Wohlleben, Jens Reuther, Malm Sven,Tiffert Yvonne,Micklinghoff Julia,Schultze Sonja,Joost Insa,Weber Isabel,Horst Sarah,Ackermann Birgit,Ehlers Stefan,Geffers Robert,Bange Franz-Christoph

Date Published: 1st Apr 2009

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

Streptomyces coelicolor GlnR is a global regulator that controls genes involved in nitrogen metabolism. By genomic screening 10 new GlnR targets were identified, including enzymes for ammonium assimilation ...

Authors: Wolfgang Wohlleben, Jens Reuther, Tiffert Yvonne,Supra Petra,Wurm Reinhild,Wagner Rolf

Date Published: 7th Jan 2008

Journal: Mol. Microbiol.

Abstract:

Not specified

Authors: William Gaze, Elizabeth Wellington, O'Neill Colette,Hawkey Peter

Date Published: 9th Apr 2008

Journal: Adv. Appl. Microbiol.

Abstract (Expand)

The prevalences of three sulfonamide resistance genes, sul1, sul2, and sul3 and sulfachloropyridazine (SCP) resistance were determined in bacteria isolated from manured agricultural clay soils and ...

Authors: William Gaze, Elizabeth Wellington, Byrne-Bailey K G,Kay P,Boxall A B A,Hawkey P M

Date Published: 8th Dec 2008

Journal: Antimicrob. Agents Chemother.

Abstract (Expand)

Metabolic models have the potential to impact on genome annotation and on the interpretation of gene expression and other high throughput genome data. The genome of Streptomyces coelicolor genome has ...

Authors: David Hodgson, David Wild, Saqi Mansoor,Dobson Richard J B,Kraben Preben

Date Published: 13th Nov 2008

Journal: J Integr Bioinform

Abstract (Expand)

SUMMARY: Systems Biology Markup Language (SBML) is the leading exchange format for mathematical models in Systems Biology. Semantic annotations link model elements with external knowledge via unique ...

Authors: Falko Krause, Edda Klipp, Uhlendorf Jannis,Lubitz Timo,Schulz Marvin,Liebermeister Wolfram

Date Published: 17th Nov 2009

Journal: Bioinformatics

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Abstract A new YNB medium containing very low concentrations of alkali metal cations has been developed to carry out experiments to study potassium homoeostasis. Physiological characterization of ...

Authors: Clara Navarrete, Silvia Petrezselyova, Lina Patricia Barreto Parra, Jaromir Zahrádka, Joaquin Ariño, Hana Sychrova, Jose Ramos, Martínez José L

Date Published: 25th May 2010

Journal: Not specified

Abstract (Expand)

The phosphatase calcineurin and the kinases Hal4/Hal5 regulate high-affinity potassium uptake in Saccharomyces cerevisiae through the Trk1 transporter. We demonstrate that calcineurin is necessary for ...

Authors: Joaquin Ariño, Jose Ramos, Casado Carlos,Yenush Lynne,Melero Carmen,Ruiz María del Carmen,Serrano Raquel,Pérez-Valle Jorge

Date Published: 3rd Jul 2009

Journal: FEBS Lett.

Abstract (Expand)

The maintenance of appropriate intracellular concentrations of alkali metal cations, principally K(+) and Na(+), is of utmost importance for living cells, since they determine cell volume, intracellular ...

Authors: None

Date Published: 4th Mar 2010

Journal: Microbiol. Mol. Biol. Rev.

Abstract (Expand)

We designed a simple graphical presentation for the results of a transcription factor (TF) pattern matching analysis. The TF analysis algorithm utilized known sequence signature motifs from several ...

Authors: None

Date Published: 19th Mar 2010

Journal: Genome Inform

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Maintenance of cation homoeostasis is a key process for any living organism. Specific mutations in Glc7, the essential catalytic subunit of yeast protein phosphatase 1, result in salt and alkaline pH ...

Authors: Clara Navarrete, Lina Patricia Barreto Parra, Jose Ramos, Joaquin Ariño, Antonio Casamayor, Ferrer-Dalmau Jofre,González Asier,Platara Maria,Martínez José L

Date Published: 24th Dec 2009

Journal: Biochem. J.

Abstract (Expand)

14-3-3 proteins form a family of highly conserved, acidic, dimeric proteins. These proteins have been identified in all eukaryotic species investigated, often in multiple isoforms, up to 13 in the plant ...

Authors: None

Date Published: 29th May 2009

Journal: Genomics

Abstract (Expand)

Defects of the mitochondrial K(+)/H(+) exchanger (KHE) result in increased matrix K(+) content, swelling, and autophagic decay of the organelle. We have previously identified the yeast Mdm38 and its ...

Authors: Rudolf Schweyen, Karin Nowikovsky, Zotova Ludmila,Aleschko Markus,Sponder Gerhard,Baumgartner Roland,Reipert Siegfried,Prinz Monika

Date Published: 2nd Mar 2010

Journal: J. Biol. Chem.

Abstract (Expand)

Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite ...

Authors: Falko Krause, Edda Klipp, Liebermeister Wolfram,Uhlendorf Jannis,Lubitz Timo

Date Published: 20th Apr 2009

Journal: Nature Precedings

Abstract (Expand)

Saccharomyces cerevisiae yeast cells serve as a model to elucidate the bases of salt tolerance and potassium homeostasis regulation in eukaryotic cells. In this study, we show that two widely used ...

Authors: None

Date Published: 1st Feb 2010

Journal: Fungal Biology

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such ...

Authors: Isabel Rojas, Renate Kania, Olga Krebs, Golebiewski Martin,Mir Saqib,Weidemann Andreas,Wittig Ulrike

Date Published: 14th Sep 2007

Journal: In Silico Biol. (Gedrukt)

Abstract (Expand)

Bacillus subtilis cells may opt to forgo normal cell division and instead form spores if subjected to certain environmental stimuli, for example nutrient deficiency or extreme temperature. The resulting ...

Authors: None

Date Published: 21st Jul 2009

Journal: Not specified

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Staphylococcus aureus is a pathogenic bacterium that utilises quorum sensing (QS), a cell-to-cell signalling mechanism, to enhance its ability to cause disease. QS allows the bacteria to monitor their ...

Authors: Sara Jabbari, John King, Koerber Adrian J,Williams Paul

Date Published: 19th Feb 2009

Journal: J Math Biol

Abstract (Expand)

Two-component systems (TCSs) are widely employed by bacteria to sense specific external signals and conduct an appropriate response via a phosphorylation cascade within the cell. The TCS of the agr ...

Authors: Sara Jabbari, John King, Williams Paul

Date Published: 30th Nov 2009

Journal: Math Biosci

Abstract (Expand)

SUMMARY: SensSB (Sensitivity Analysis for Systems Biology) is an easy to use, MATLAB-based software toolbox, which integrates several local and global sensitivity methods that can be applied to a wide ...

Authors: None

Date Published: 7th May 2010

Journal: Not specified

Abstract (Expand)

The regulatory proteins AfsR and PhoP control expression of the biosynthesis of actinorhodin and undecylprodigiosin in Streptomyces coelicolor. Electrophoretic mobility shift assays showed that PhoP(DBD) ...

Authors: Antonio Rodríguez-García, Juan-Francisco Martin, Santos-Beneit Fernando,Sola-Landa Alberto

Date Published: 11th Feb 2009

Journal: Mol. Microbiol.

Abstract (Expand)

Stability and biological activity of proteins is highly dependent on their physicochemical environment. The development of realistic models of biological systems necessitates quantitative information ...

Authors: Ana Kitanovic, Peter Ruoff, Stefan Wölfl, Bonowski Felix,Holzwarth Jinda,Kitanovic Igor,Bui Van Ngoc,Lederer Elke

Date Published: 23rd Dec 2009

Journal: PLoS ONE

Abstract (Expand)

Systems Biology has a mission that puts it at odds with traditional paradigms of physics and molecular biology, such as the simplicity requested by Occam's razor and minimum energy/maximal efficiency. ...

Authors: Hans Westerhoff, Hanan Messiha, Malkhey Verma, Winder Catherine,Simeonidis Evangelos,Adamczyk Malgorzata,Bruggeman Frank J,Dunn Warwick

Date Published: 6th Nov 2009

Journal: FEBS Lett.

Abstract (Expand)

The roles of the two ldh genes of Enterococcus faecalis were studied using knockout mutants. Deletion of ldh-1 causes a metabolic shift from homolactic fermentation to ethanol, formate, and acetoin ...

Authors: Maria Jonsson, Ingolf Nes, Helge Holo, Saleihan Zhian

Date Published: 22nd May 2009

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Appropriate stimulus perception, signal processing and transduction ensure optimal adaptation of bacteria to environmental challenges. In the Gram-positive model bacterium Bacillus subtilis signalling ...

Authors: None

Date Published: 1st Jul 2010

Journal: Not specified

Abstract (Expand)

African trypanosomes have emerged as promising unicellular model organisms for the next generation of systems biology. They offer unique advantages, due to their relative simplicity, the availability ...

Authors: Barbara Bakker, Luise Krauth-Siegel, Christine Clayton, Keith Matthews, Mark Girolami, Hans Westerhoff, Rainer Breitling, Mike Barrett, Michels Paul A M

Date Published: 6th May 2010

Journal: Parasitology

Abstract (Expand)

Metabolomics analysis, which aims at the systematic identification and quantification of all metabolites in biological systems, is emerging as a powerful new tool to identify biomarkers of disease, ...

Authors: None

Date Published: 17th Feb 2010

Journal: Parasitology

Abstract (Expand)

Summary The PrsA protein is a membrane-anchored peptidyl-prolyl cis-trans isomerase in Bacillus subtilis and most other Gram-positive bacteria. It catalyses the post-translocational folding of exported ...

Authors: Bogumila Marciniak, Oscar Kuipers, Hyyryläinen Hanne-Leena,Dahncke Kathleen,Pietiäinen Milla,Courtin Pascal,Vitikainen Marika,Seppala Raili,Otto Andreas,Becher Dörte,Chapot-Chartier Marie-Pierre,Kontinen Vesa P

Date Published: 4th May 2010

Journal: Mol. Microbiol.

Abstract (Expand)

The general stress regulon of Bacillus subtilis is controlled by the activity state of sigmaB, a transcription factor that is switched on following exposure to either physical or nutritional stress. ...

Authors: Uwe Voelker, Reeves Adam,Gerth Ulf,Haldenwang W G

Date Published: 22nd Jun 2007

Journal: J. Bacteriol.

Abstract (Expand)

Catechol and 2-methylhydroquinone (2-MHQ) cause the induction of the thiol-specific stress response and four dioxygenases/glyoxalases in Bacillus subtilis. Using transcription factor arrays, the MarR-type ...

Authors: Michael Hecker, Töwe Stefanie,Leelakriangsak Montira,Kobayashi Kazuo,Van Duy Nguyen,Zuber Peter,Antelmann Haike

Date Published: 27th Aug 2007

Journal: Mol. Microbiol.

Abstract (Expand)

Recently, we showed that the MarR-type repressor YkvE (MhqR) regulates multiple dioxygenases/glyoxalases, oxidoreductases and the azoreductase encoding yvaB (azoR2) gene in response to thiol-specific ...

Authors: Michael Hecker, Leelakriangsak Montira,Huyen Nguyen Thi Thu,Töwe Stefanie,van Duy Nguyen,Becher Dörte,Antelmann Haike,Zuber Peter

Date Published: 16th Jan 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Proteomic and transcriptomics signatures are powerful tools for visualizing global changes in gene expression in bacterial cells after exposure to stress, starvation or toxic compounds. Based on the ...

Authors: Michael Hecker, Antelmann Haike,Zuber Peter

Date Published: 20th Feb 2008

Journal: Not specified

Abstract (Expand)

The twin arginine translocation (Tat) system transports folded proteins across the bacterial plasma membrane. In Gram-negative bacteria, membrane-bound TatABC subunits are all essential for activity, ...

Authors: Oscar Kuipers, Jan Maarten Van Dijl, Barnett James P,van der Ploeg René,Eijlander Robyn T,Nenninger Anja,Mendel Sharon,Rozeboom Rense,Robinson Colin

Date Published: 25th Nov 2008

Journal: FEBS J.

Abstract (Expand)

Glutamate is a central metabolite in all organisms since it provides the link between carbon and nitrogen metabolism. In Bacillus subtilis, glutamate is synthesized exclusively by the glutamate synthase, ...

Authors: Joerg Stuelke, Commichau Fabian M,Gunka Katrin,Landmann Jens J

Date Published: 7th Mar 2008

Journal: J. Bacteriol.

Abstract (Expand)

Bacillus subtilis has been developed as a model system for physiological proteomics. However, thus far these studies have mainly been limited to cytoplasmic, extracellular, and cell-wall attached ...

Authors: Michael Hecker, Uwe Voelker, Dreisbach Annette,Otto Andreas,Becher Dörte,Hammer Elke,Teumer Alexander,Gouw Joost W

Date Published: 21st May 2008

Journal: Proteomics

Abstract (Expand)

We investigate design principles of linear multi-stage phosphorylation cascades by using quantitative measures for signaling time, signal duration and signal amplitude. We compare alternative pathway ...

Authors: Thomas Millat, Olaf Wolkenhauer, Frey Simone,Hohmann Stefan

Date Published: 6th Sep 2007

Journal: J. Theor. Biol.

Abstract (Expand)

Most bacteria can selectively use substrates from a mixture of different carbon sources. The presence of preferred carbon sources prevents the expression, and often also the activity, of catabolic ...

Authors: Joerg Stuelke, Görke Boris

Date Published: 17th Jul 2008

Journal: Nat. Rev. Microbiol.

Abstract (Expand)

In this review, we demonstrate the power of gel-based proteomics to address physiological questions of bacteria. Although gel-based proteomics covers a subpopulation of proteins only, fundamental issues ...

Authors: Michael Hecker, Antelmann Haike,Büttner Knut,Bernhardt Jörg

Date Published: 13th Nov 2008

Journal: Proteomics

Abstract (Expand)

Protein degradation mediated by ATP-dependent proteases, such as Hsp100/Clp and related AAA+ proteins, plays an important role in cellular protein homeostasis, protein quality control and the regulation ...

Authors: Leendert Hamoen, Kirstein Janine,Strahl Henrik,Molière Noël,Turgay Kürşad

Date Published: 10th Sep 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Thiol-disulfide oxidoreductases (TDORs) catalyze thiol-disulfide exchange reactions that are crucial for protein activity and stability. Specifically, they can function as thiol oxidases, disulfide ...

Authors: Jan Maarten Van Dijl, Kouwen Thijs R H M

Date Published: 30th May 2008

Journal: Trends Microbiol.

Abstract (Expand)

Disulfide bonds are important for the correct folding, structural integrity, and activity of many biotechnologically relevant proteins. For synthesis and subsequent secretion of these proteins in ...

Authors: Jan Maarten Van Dijl, Kouwen Thijs R H M,Dubois Jean-Yves F,Freudl Roland,Quax Wim J

Date Published: 24th Oct 2008

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Bistable systems play an important role in the functioning of living cells. Depending on the strength of the necessary positive feedback one can distinguish between (irreversible) "one-way ...

Authors: Thomas Millat, Olaf Wolkenhauer, Sreenath Sree N,Soebiyanto Radina P,Avva Jayant,Cho Kwang-Hyun

Date Published: 17th Jan 2007

Journal: BioSystems

Abstract (Expand)

In many bacteria glucose is the preferred carbon source and represses the utilization of secondary substrates. In Bacillus subtilis, this carbon catabolite repression (CCR) is achieved by the global ...

Authors: Joerg Stuelke, Singh Kalpana D,Schmalisch Matthias H,Görke Boris

Date Published: 29th Aug 2008

Journal: J. Bacteriol.

Abstract (Expand)

The alternative sigma factor sigma(B) of Bacillus subtilis is responsible for the induction of the large general stress regulon comprising approximately 150-200 genes. YqgZ, a member of the sigma(B) ...

Authors: Michael Hecker, Reder Alexander,Höper Dirk,Weinberg Christin,Gerth Ulf,Fraunholz Martin

Date Published: 14th Jul 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Bacillus subtilis is a prolific producer of enzymes and biopharmaceuticals. However, the susceptibility of heterologous proteins to degradation by (extracellular) proteases is a major limitation for ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Westers Lidia,Westers Helga,Zanen Geeske,Antelmann Haike,Noone David,Devine Kevin M,Quax Wim J

Date Published: 12th Jun 2008

Journal: Proteomics

Abstract (Expand)

ABSTRACT: BACKGROUND: The Gram-positive bacterium Bacillus subtilis is an important producer of high quality industrial enzymes and a few eukaryotic proteins. Most of these proteins are secreted into ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Zweers Jessica C,Barák Imrich,Becher Dörte,Driessen Arnold Jm,Kontinen Vesa P,Saller Manfred J,Vavrová L'udmila

Date Published: 2nd Dec 2007

Journal: Microb. Cell Fact.

Abstract (Expand)

Bacillus subtilis strain 168 produces the extremely stable lantibiotic sublancin 168, which has a broad spectrum of bactericidal activity. Both sublancin 168 production and producer immunity are ...

Authors: Jan Maarten Van Dijl, Dubois Jean-Yves F,Kouwen Thijs R H M,Schurich Anna K C,Reis Carlos R,Ensing Hendrik T,Trip Erik N,Zweers Jessica C

Date Published: 1st Dec 2008

Journal: Antimicrob. Agents Chemother.

Abstract (Expand)

Quinones and alpha,beta-unsaturated carbonyls are naturally occurring electrophiles that target cysteine residues via thiol-(S)-alkylation. We analysed the global expression profile of Bacillus subtilis ...

Authors: Michael Lalk, Michael Hecker, Nguyen Thi Thu Huyen,Eiamphungporn Warawan,Mäder Ulrike,Liebeke Manuel,Helmann John D,Antelmann Haike

Date Published: 23rd Dec 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Bacteria secrete numerous proteins into their environment for growth and survival under complex and ever-changing conditions. The highly different characteristics of secreted proteins pose major ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Kouwen Thijs R H M,van der Ploeg René,Antelmann Haike,Homuth Georg,Mäder Ulrike

Date Published: 31st Jan 2009

Journal: Proteomics

Abstract (Expand)

Bacillus subtilis serves as an excellent model to study protein secretion at a proteomic scale. Most of the extracellular proteins are exported from the cytoplasm via the secretory (Sec) pathway. Despite ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Kouwen Thijs R H M,Antelmann Haike,van der Ploeg René,Denham Emma L

Date Published: 23rd Jan 2009

Journal: Proteomics

Abstract (Expand)

Phosphorylation is an important mechanism of protein modification. In the Gram-positive soil bacterium Bacillus subtilis, about 5% of all proteins are subject to phosphorylation, and a significant ...

Authors: Michael Hecker, Joerg Stuelke, Pietack Nico,Becher Dörte,Schmidl Sebastian R,Saier Milton H,Commichau Fabian M

Date Published: 13th Apr 2010

Journal: J. Mol. Microbiol. Biotechnol.

Abstract (Expand)

We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive linear ...

Authors: Oscar Kuipers, Brouwer Rutger W W,van Hijum Sacha A F T

Date Published: 12th Nov 2008

Journal: Bioinformatics

Abstract (Expand)

Glycolysis is one of the most important metabolic pathways in heterotrophic organisms. Several genes encoding glycolytic enzymes are essential in many bacteria even under conditions when neither ...

Authors: Uwe Voelker, Joerg Stuelke, Commichau Fabian M,Rothe Fabian M,Herzberg Christina,Wagner Eva,Hellwig Daniel,Lehnik-Habrink Martin,Hammer Elke

Date Published: 3rd Feb 2009

Journal: Mol. Cell Proteomics

Abstract (Expand)

In response to limiting nutrient sources and cell density signals, Bacillus subtilis can differentiate and form highly resistant endospores. Initiation of spore development is governed by the master ...

Authors: None

Date Published: 12th Feb 2010

Journal: J. Bacteriol.

Abstract (Expand)

Bacillus subtilis is the model organism for Gram-positive bacteria, with a large amount of publications on all aspects of its biology. To facilitate genome annotation and the collection of comprehensive ...

Authors: Lope A. Florez, Joerg Stuelke, Roppel Sebastian F,Schmeisky Arne G,Lammers Christoph R

Date Published: 26th May 2009

Journal: Not specified

Abstract (Expand)

Bacillus subtilis strain 168 produces the extremely stable and broad-spectrum lantibiotic sublancin 168. Known sublancin 168-susceptible organisms include important pathogens, such as Staphylococcus ...

Authors: Jan Maarten Van Dijl, Kouwen Thijs R H M,Trip Erik N,Denham Emma L,Sibbald Mark J J B,Dubois Jean-Yves F

Date Published: 8th Sep 2009

Journal: Antimicrob. Agents Chemother.

Abstract (Expand)

Bacillus subtilis is a well-established cellular factory for proteins and fine chemicals. In particular, the direct secretion of proteinaceous products into the growth medium greatly facilitates their ...

Authors: Jan Maarten Van Dijl, Kouwen Thijs R H M

Date Published: 11th Jun 2009

Journal: Appl. Microbiol. Biotechnol.

Abstract (Expand)

Bacillus subtilis is a well-established cell factory for efficient secretion of many biotechnologically relevant enzymes that are naturally produced by it or related organisms. However, the use of B. ...

Authors: Jan Maarten Van Dijl, Kouwen Thijs R H M,Nielsen Allan K,Denham Emma L,Dubois Jean-Yves F,Dorenbos Ronald,Rasmussen Michael D,Quax Wim J,Freudl Roland

Date Published: 30th Nov 2009

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Bacillus subtilis is the model organism for a large group of Gram-positive bacteria, the Firmicutes. Several online databases have been established over time to manage its genetic and metabolic ...

Authors: Lope A. Florez, Leendert Hamoen, Joerg Stuelke, Lammers Christoph R,Schmeisky Arne G,Roppel Sebastian F,Mäder Ulrike

Date Published: 3rd Dec 2009

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

Analysis of metabolome samples by gas chromatography/mass spectrometry requires a comprehensive derivatization method to afford quantitative and qualitative information of a complex biological sample. ...

Authors: Michael Lalk, Liebeke Manuel,Wunder Ariane

Date Published: 4th Feb 2009

Journal: Anal. Biochem.

Abstract (Expand)

Glutathione constitutes a key player in the thiol redox buffer in many organisms. However, the gram-positive bacteria Bacillus subtilis and Staphylococcus aureus lack this low-molecular-weight thiol. ...

Authors: Michael Lalk, Michael Hecker, Pöther Dierk-Christoph,Liebeke Manuel,Hochgräfe Falko,Antelmann Haike,Becher Dörte,Lindequist Ulrike,Borovok Ilya,Cohen Gerald,Aharonowitz Yair

Date Published: 16th Oct 2009

Journal: J. Bacteriol.

Abstract (Expand)

A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been ...

Authors: Oscar Kuipers, van Hijum Sacha A F T,Medema Marnix H

Date Published: 2nd Sep 2009

Journal: Microbiol. Mol. Biol. Rev.

Abstract (Expand)

In the three domains of life, the Sec, YidC/Oxa1, and Tat translocases play important roles in protein translocation across membranes and membrane protein insertion. While extensive studies have been ...

Authors: Jan Maarten Van Dijl, Yuan Jijun,Zweers Jessica C,Dalbey Ross E

Date Published: 16th Jun 2009

Journal: Cell. Mol. Life Sci.

Abstract (Expand)

Essential membrane proteins are generally recognized as relevant potential drug targets due to their exposed localization in the cell envelope. Unfortunately, high-level production of membrane proteins ...

Authors: Jan Maarten Van Dijl, Zweers Jessica C,Wiegert Thomas

Date Published: 9th Oct 2009

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Any signal transduction requires communication between a sensory component and an effector. Some enzymes engage in signal perception and transduction, as well as in catalysis, and these proteins are ...

Authors: Joseph Newman, Rick Lewis, Gunka Katrin,Commichau Fabian M,Herzberg Christina,Rodrigues Cecilia,Hewitt Lorraine,Stülke Jörg

Date Published: 22nd Feb 2010

Journal: J. Mol. Biol.

Abstract (Expand)

Gel-based proteomics is a useful approach for visualizing the responses of bacteria to stress and starvation stimuli. In order to face stress/starvation, bacteria have developed very complicated gene ...

Authors: Michael Hecker, Reder Alexander,Fuchs Stephan,Pagels Martin,Engelmann Susanne

Date Published: 20th Feb 2009

Journal: Res. Microbiol.

Abstract (Expand)

SUMMARY: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now ...

Authors: Matthew Rolfe, Jeff Green, Guido Sanguinetti, Asif H M Shahzad,Lawrence Neil D,Rattray Magnus

Date Published: 24th Aug 2010

Journal: Bioinformatics

Abstract (Expand)

In this article we present and test a strategy to integrate, in a sequential manner, sensitivity analysis, bifurcation analysis and predictive simulations. Our strategy uses some of these methods in a ...

Authors: Ulf Liebal, Olaf Wolkenhauer, Nikolov S.,Lai X.,Vera J.

Date Published: 2010

Journal: Int. J. of Systems Sc.

Abstract (Expand)

Background Signalling pathways are complex systems in which not only simple monomeric molecules interact, but also more complex structures that include constitutive or induced protein assemblies. In ...

Authors: Thomas Millat, Olaf Wolkenhauer, Vera Julio,Kolch Walter

Date Published: 2008

Journal: BMC Syst Biol

Abstract (Expand)

The following article describes systems biology as a merger of systems theory with cell biology. The role of modelling in the description of living cells is discussed. As an example, an abstract ...

Authors: Olaf Wolkenhauer, Hofmeyr Jan-Hendrik S.

Date Published: 1st May 2008

Journal: at - Automatisierungstechnik

Abstract (Expand)

The complex changes in the life cycle of Clostridium acetobutylicum, a promising biofuel producer, are not well understood. During exponential growth, sugars are fermented to acetate and butyrate, and ...

Authors: Holger Janssen, Christina Döring, Armin Ehrenreich, Hubert Bahl, Ralf-Jörg Fischer, Voigt Birgit,Hecker Michael

Date Published: 1st Aug 2010

Journal: Appl Microbiol Biotechnol

Abstract (Expand)

The majority of all proteins of a living cell is active in complexes rather than in an isolated way. These protein-protein interactions are of high relevance for many biological functions. In addition ...

Authors: Uwe Voelker, Joerg Stuelke, Meyer Frederik M,Gerwig Jan,Hammer Elke,Herzberg Christina,Commichau Fabian M

Date Published: 20th Aug 2010

Journal: Not specified

Abstract (Expand)

Fluorescence microscopy is an imaging technique that provides insights into signal transduction pathways through the generation of quantitative data, such as the spatiotemporal distribution of GFP-tagged ...

Authors: Thomas Millat, Olaf Wolkenhauer, Frey Simone,Sott Kristin,Smedh Maria,Dahl Peter,Goksör Mattias

Date Published: 2011

Journal: Mol. BioSyst.

Abstract (Expand)

Several lactic acid bacteria use homolactic fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three homolactic acid ...

Authors: Tomas Fiedler, Martijn Bekker, Maria Jonsson, Ibrahim Mehmeti, Ingolf Nes, Jeroen Hugenholtz, Bernd Kreikemeyer, Pritzschke Anja,Siemens Nikolai

Date Published: 25th Nov 2010

Journal: Not specified

Abstract (Expand)

Background: Clostridium acetobutylicum is an anaerobic bacterium which is known for its solvent-producing capabilities, namely regarding the bulk chemicals acetone and butanol, the latter being a highly ...

Authors: None

Date Published: 2011

Journal: BMC Syst Biol

Abstract (Expand)

Systems biology is a comprehensive quantitative analysis how the components of a biological system interact over time which requires an interdisciplinary team of investigators. System-theoretic methods ...

Authors: None

Date Published: 11th Nov 2010

Journal: Methods Mol. Biol.

Abstract (Expand)

Oxygen availability is the major determinant of the metabolic modes adopted by Escherichia coli. Whilst much is known about E. coli gene expression and metabolism under fully aerobic and anaerobic ...

Authors: Matthew Rolfe, Alexander Ter Beek, Alison Graham, Joost Teixeira De Mattos, Robert Poole, Jeff Green, Trotter Eleanor W,Asif H M Shahzad,Sanguinetti Guido

Date Published: 22nd Jan 2011

Journal: Not specified

Abstract (Expand)

Streptococcus pyogenes (group A Streptococcus [GAS]) is a major human pathogen, causing diseases ranging from mild superficial infections of the skin and pharyngeal mucosal membrane, up to severe ...

Authors: Tomas Fiedler, Bernd Kreikemeyer, Sugareva Venelina,Patenge Nadja

Date Published: 8th Dec 2010

Journal: Future Microbiol

Abstract (Expand)

Transcription is the first step of gene expression and is characterized by a high fidelity of RNA synthesis. During transcription, the RNA polymerase active centre discriminates against not just ...

Authors: Yulia Yuzenkova, Nikolay Zenkin, Bochkareva Aleksandra,Tadigotla Vasisht R,Roghanian Mohammad,Zorov Savva,Severinov Konstantin

Date Published: 1st Apr 2010

Journal: BMC Biol.

Abstract (Expand)

How cultures of genetically identical cells bifurcate into distinct phenotypic subpopulations under uniform growth conditions is an important question in developmental biology of relevance even to ...

Authors: None

Date Published: 10th Mar 2010

Journal: Mol. Microbiol.

Abstract (Expand)

Mutations in DNA replication initiator genes in both prokaryotes and eukaryotes lead to a pleiotropic array of phenotypes, including defects in chromosome segregation, cytokinesis, cell cycle regulation ...

Authors: Jan-Willem Veening, Scholefield Graham,Murray Heath

Date Published: 27th Aug 2010

Journal: Trends Cell Biol.

Abstract (Expand)

Domesticated laboratory strains of Bacillus subtilis readily take up and integrate exogenous DNA. In contrast, "wild" ancestors or Bacillus strains recently isolated from the environment can ...

Authors: Jan-Willem Veening, Nijland Reindert,Burgess J Grant,Errington Jeff

Date Published: 11th Jan 2010

Journal: PLoS ONE

Abstract (Expand)

The molecular mechanisms underlying cell growth, cell division and pathogenesis in Streptococcus pneumoniae are still not fully understood. Single-cell methodologies are potentially of great value to ...

Authors: Jan-Willem Veening, Eberhardt Alice,Wu Ling J,Errington Jeff,Vollmer Waldemar

Date Published: 8th Sep 2009

Journal: Mol. Microbiol.

Abstract (Expand)

Coordination of DNA replication with cellular development is a crucial problem in most living organisms. Bacillus subtilis cells switch from vegetative growth to sporulation when starved. Sporulation ...

Authors: Jan-Willem Veening, Murray Heath,Errington Jeff

Date Published: 18th Aug 2009

Journal: Genes Dev.

Abstract (Expand)

The highly processive transcription by multi-subunit RNA polymerases (RNAP) can be interrupted by misincorporation or backtracking events that may stall transcription or lead to erroneous transcripts. ...

Authors: Yulia Yuzenkova, Nikolay Zenkin, Roghanian Mohammad

Date Published: 27th Jan 2011

Journal: Not specified

Abstract (Expand)

A constructed lactate dehydrogenase-negative mutant of Enterococcus faecalis V583 grows at the same rate as the wild type, but ferments glucose to ethanol, formate, and acetoin. Microrray analysis ...

Authors: Ibrahim Mehmeti, Maria Jonsson, Ingolf Nes, Helge Holo, Fergestad Ellen M,Mathiesen Geir

Date Published: 8th Feb 2011

Journal: Not specified

Abstract (Expand)

The active center of RNA polymerase can hydrolyze phosphodiester bonds in nascent RNA, a reaction thought to be important for proofreading of transcription. The reaction proceeds via a general two ...

Authors: Nikolay Zenkin, Yuzenkova Yulia

Date Published: 1st Jun 2010

Journal: Proc. Natl. Acad. Sci. U.S.A.

Abstract (Expand)

This Letter addresses the statistical significance of structures in random data: given a set of vectors and a measure of mutual similarity, how likely is it that a subset of these vectors forms a cluster ...

Authors: Johannes Berg, Łuksza Marta,Lässig Michael

Date Published: 27th Nov 2009

Journal: Phys. Rev. Lett.

Abstract (Expand)

In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR ...

Authors: Maike Bartholomae, Wolfgang Hillen, Schumacher Maria A,Sprehe Mareen,Brennan Richard G

Date Published: 26th Nov 2010

Journal: Nucleic Acids Res.

Abstract (Expand)

Within the archaea, the thermoacidophilic crenarchaeote Sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, ...

Authors: Melanie Zaparty, Susanne Gertig, Patrick Haferkamp, Theresa Kouril, Andrea Manica, Trong Khoa Pham, Kerstin Schreiber, Pawel Sierocinski, Mathias Von Jan, Patricia Wieloch, Sonja-Verena Albers, Arnold Driessen, Hans-Peter Klenk, Christa Schleper, Dietmar Schomburg, John Van Der Oost, Phil Wright, Bettina Siebers, Esser Dominik,Reimann Julia,Teichmann Daniela,van Wolferen Marleen

Date Published: 31st Aug 2009

Journal: Extremophiles

Abstract (Expand)

Various types of the staphylococcal cassette chromosome mec (SCCmec) are known to confer methicillin resistance on the human pathogen Staphylococcus aureus. Such cassettes are not always stably maintained. ...

Authors: Jan Maarten Van Dijl, Chlebowicz Monika A,Nganou Kristelle,Kozytska Svitlana,Arends Jan P,Engelmann Susanne,Grundmann Hajo,Ohlsen Knut,Buist Girbe

Date Published: 7th Dec 2009

Journal: Antimicrob. Agents Chemother.

Abstract (Expand)

The important human pathogen Staphylococcus aureus is known to spread on soft agar plates. Here, we show that colony spreading of S. aureus involves the agr quorum-sensing system. This finding can be ...

Authors: Jan Maarten Van Dijl, Tsompanidou Eleni,Sibbald Mark J J B,Chlebowicz Monika A,Dreisbach Annette,Back Jaap Willem,Buist Girbe,Denham Emma L

Date Published: 17th Dec 2010

Journal: J. Bacteriol.

Abstract (Expand)

In eukaryotic cell types, virtually all cellular processes are under control of proline-directed kinases and especially MAP kinases. Serine/threonine kinases in general were originally considered as a ...

Authors: Jan Maarten Van Dijl, Miller Malgorzata,Donat Stefanie,Rakette Sonja,Stehle Thilo,Kouwen Thijs R H M,Diks Sander H,Dreisbach Annette,Reilman Ewoud,Gronau Katrin,Becher Dörte,Peppelenbosch Maikel P,Ohlsen Knut

Date Published: 12th Nov 2009

Journal: PLoS ONE

Abstract (Expand)

The budding yeast Saccharomyces cerevisiae grows far better at acidic than at neutral or alkaline pH. Consequently, even a modest alkalinization of the medium represents a stressful situation for this ...

Authors: None

Date Published: 20th Aug 2010

Journal: OMICS

Abstract (Expand)

To maintain optimal intracellular concentrations of alkali-metal-cations, yeast cells use a series of influx and efflux systems. Nonconventional yeast species have at least three different types of ...

Authors: None

Date Published: 1st Feb 2011

Journal: FEMS Microbiol. Lett.

Abstract (Expand)

We determined the diffusion coefficients (D) of (macro)molecules of different sizes (from ∼0.5 to 600 kDa) in the cytoplasm of live Escherichia coli cells under normal osmotic conditions and osmotic ...

Authors: Jacek Mika, Bert Poolman, Van Den Bogaart Geert,Veenhoff Liesbeth,Krasnikov Victor

Date Published: 1st Jul 2010

Journal: Not specified

Abstract (Expand)

We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the ...

Authors: None

Date Published: 16th Oct 2010

Journal: Curr. Opin. Biotechnol.

Abstract (Expand)

The effect of osmotic stress on the intracellular diffusion of proteins in Escherichia coli was studied, using a pulsed version of fluorescence recovery after photo-bleaching, pulsed-FRAP. This method ...

Authors: Bert Poolman, van den Bogaart Geert,Hermans Nicolaas,Krasnikov Victor

Date Published: 28th Apr 2007

Journal: Mol. Microbiol.

Abstract (Expand)

We have developed a general scenario of prebiotic physicochemical evolution during the Earth's Hadean eon and reviewed the relevant literature. We suggest that prebiotic chemical evolution started ...

Authors: Bert Poolman, Spitzer Jan

Date Published: 3rd Jun 2009

Journal: Microbiol. Mol. Biol. Rev.

Abstract (Expand)

We report the molecular basis for the differences in activity of cyclic and linear antimicrobial peptides. We iteratively performed atomistic molecular dynamics simulations and biophysical measurements ...

Authors: Jacek Mika, Bert Poolman, Moiset Gemma,Cirac Anna D,Feliu Lidia,Bardají Eduard,Planas Marta,Sengupta Durba,Marrink Siewert J

Date Published: 19th May 2011

Journal: Not specified

Abstract (Expand)

The mechanism of action of antimicrobial peptides is, to our knowledge, still poorly understood. To probe the biophysical characteristics that confer activity, we present here a molecular-dynamics and ...

Authors: Jacek Mika, Bert Poolman, Cirac Anna D,Moiset Gemma,Koçer Armagan,Salvador Pedro,Marrink Siewert J,Sengupta Durba

Date Published: 18th May 2011

Journal: Biophys. J.

Abstract (Expand)

Segregation of replicated chromosomes is an essential process in all organisms. How bacteria, such as the oval-shaped human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes ...

Authors: Jan-Willem Veening, Minnen Anita,Attaiech Laetitia,Thon Maria,Gruber Stephan

Date Published: 22nd Jun 2011

Journal: Mol. Microbiol.

Abstract (Expand)

During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of ...

Authors: Imke De Jong, Oscar Kuipers, Jan-Willem Veening, Beilharz Katrin

Date Published: 16th Aug 2011

Journal: J Vis Exp

Abstract (Expand)

Enterococcus faecalis V583 was grown in a glucose-limited chemostat at three different (0.05 h(-1), 0.15 h(-1) and 0.4 h(-1)) growth rates. The fermentation pattern changed with growth rate, from a ...

Authors: Ibrahim Mehmeti, Martijn Bekker, Ingolf Nes, Helge Holo, Faergestad Ellen M,Snipen Lars

Date Published: 1st Nov 2011

Journal: Applied and environmental microbiology

Abstract (Expand)

Bacterial promoters are recognized by RNA polymerase (RNAP) σ subunit, which specifically interacts with the -10 and -35 promoter elements. Here, we provide evidence that the β' zipper, an ...

Authors: Yulia Yuzenkova, Nikolay Zenkin, Tadigotla Vasisht R,Severinov Konstantin

Date Published: 26th Jul 2011

Journal: EMBO J.

Abstract (Expand)

Pausing of transcription is an important step of regulation of gene expression in bacteria and eukaryotes. Here we uncover a factor-independent mechanism of transcription pausing, which is determined ...

Authors: Yulia Yuzenkova, Nikolay Zenkin, Bochkareva Aleksandra,Tadigotla Vasisht R

Date Published: 29th Nov 2011

Journal: EMBO J.

Abstract (Expand)

Transcription and translation are coupled in bacteria, meaning that translation takes place co-transcriptionally. During transcription-translation, both machineries mutually affect each others' ...

Authors: Nikolay Zenkin, Castro-Roa Daniel

Date Published: 3rd Jan 2012

Journal: Nucleic acids research

Abstract (Expand)

Genes are regulated because their expression involves a fitness cost to the organism. The production of proteins by transcription and translation is a well-known cost factor, but the enzymatic activity ...

Authors: Johannes Berg, Perfeito Lilia,Ghozzi Stéphane,Schnetz Karin,Lässig Michael

Date Published: 21st Jul 2011

Journal: PLoS Genet.

Abstract (Expand)

Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the ...

Authors: None

Date Published: 19th Jan 2012

Journal: PLoS Comput Biol

Abstract (Expand)

Lactic acid-producing bacteria survive in distinct environments, but show common metabolic characteristics. Here we studied the dynamic interactions of the central metabolism in Lactococcus lactis, ...

Authors: None

Date Published: 14th Feb 2012

Journal: The FEBS journal

Abstract (Expand)

In the field of metabolomics, GC–MS has rather established itself as a tool for semi-quantitative strategies like metabolic fingerprinting or metabolic profiling. Absolute quantification of intra- or ...

Authors: Maksim Zakhartsev, Matthias Reuss, Vielhauer Oliver,Horn Thomas,Takors Ralf

Date Published: 1st Dec 2011

Journal: Journal of Chromatography B

Abstract (Expand)

Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be ...

Authors: None

Date Published: 29th Sep 2011

Journal: Meth. Enzymol.

Abstract (Expand)

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, ...

Authors: Katy Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Müller, Jacky Snoep, Franco Du Preez, Carole Goble, Horridge Matthew

Date Published: 26th May 2011

Journal: Bioinformatics

Abstract (Expand)

BACKGROUND: Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin ...

Authors: Stuart Owen, Katy Wolstencroft, Jupp Simon,Horridge Matthew,Iannone Luigi,Klein Julie,Schanstra Joost,Stevens Robert

Date Published: 25th Jan 2012

Journal: BMC bioinformatics

Abstract (Expand)

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' ...

Authors: Carole Goble, Katy Wolstencroft, Sansone Susanna-Assunta,Rocca-Serra Philippe,Field Dawn,Maguire Eamonn,Taylor Chris,Hofmann Oliver,Fang Hong,Neumann Steffen,Tong Weida,Amaral-Zettler Linda,Begley Kimberly,Booth Tim,Bougueleret Lydie,Burns Gully,Chapman Brad,Clark Tim,Coleman Lee-Ann,Copeland Jay,Das Sudeshna,de Daruvar Antoine,de Matos Paula,Dix Ian,Edmunds Scott,Evelo Chris T,Forster Mark J,Gaudet Pascale,Gilbert Jack,Griffin Julian L,Jacob Daniel,Kleinjans Jos,Harland Lee,Haug Kenneth,Hermjakob Henning,Ho Sui Shannan J,Laederach Alain,Liang Shaoguang,Marshall Stephen,McGrath Annette,Merrill Emily,Reilly Dorothy,Roux Magali,Shamu Caroline E,Shang Catherine A,Steinbeck Christoph,Trefethen Anne,Williams-Jones Bryn,Xenarios Ioannis,Hide Winston

Date Published: 28th Jan 2012

Journal: Nat. Genet.

Abstract (Expand)

Clostridium acetobutylicum is able to switch from acidogenic growth to solventogenic growth. We used phosphate-limited continuous cultures that established acidogenic growth at pH 5.8 and solventogenic ...

Authors: Holger Janssen, Désireé Krausse, Ralf-Jörg Fischer, Hubert Bahl, Peter Dürre, Armin Ehrenreich, Grimmler Christina,Liebl Wolfgang

Date Published: 6th Jan 2011

Journal: J. Mol. Microbiol. Biotechnol.

Abstract (Expand)

How the human pathogen Streptococcus pneumoniae coordinates cell-wall synthesis during growth and division to achieve its characteristic oval shape is poorly understood. The conserved eukaryotic-type ...

Authors: Jan-Willem Veening, Beilharz Katrin,Nováková Linda,Fadda Daniela,Branny Pavel,Massidda Orietta

Date Published: 21st Mar 2012

Journal: Proceedings of the National Academy of Sciences of the United States of America

Abstract (Expand)

In vivo nuclear magnetic resonance (NMR) monitoring requires a high-density cell suspension, where cell precipitation should be avoided. We have designed a miniaturized cell agitator that fits entirely ...

Authors: Maksim Zakhartsev, Bock Christian

Date Published: 1st Feb 2010

Journal: Analytical Biochemistry

Abstract:

Not specified

Authors: Sonja Steinsiek, Stefan Stagge, Katja Bettenbrock, Frixel S.

Date Published: 1st Jun 2011

Journal: Journal of Biotechnology

Abstract (Expand)

To gain more insight into the butanol stress response of Clostridium acetobutylicum the transcriptional response of a steady state acidogenic culture to different levels of n-butanol (0.25-1%) was ...

Authors: Katrin Schwarz, Wouter Kuit, Armin Ehrenreich, Servé Kengen, Grimmler Christina

Date Published: 1st Mar 2012

Journal: Journal of Biotechnology

Abstract:

Not specified

Authors: Matthias Reuss, Schaub Jochen,Schiesling Carola,Dauner Michael

Date Published: 2006

Journal: Biotechnol Progress

Abstract (Expand)

Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report ...

Authors: Ulrike Mäder, Colin Harwood, Rick Lewis, Ruben Mars, Priyanka Nannapaneni, Praveen Kumar Sappa, Leif Steil, Joerg Stuelke, Jan Maarten Van Dijl, Michael Hecker, Uwe Voelker, Nicolas Pierre,Dervyn Etienne,Rochat Tatiana,Leduc Aurélie,Pigeonneau Nathalie,Bidnenko Elena,Marchadier Elodie,Hoebeke Mark,Aymerich Stéphane,Becher Dörte,Bisicchia Paola,Botella Eric,Delumeau Olivier,Doherty Geoff,Denham Emma L,Fogg Mark J,Fromion Vincent,Goelzer Anne,Hansen Annette,Härtig Elisabeth,Homuth Georg,Jarmer Hanne,Jules Matthieu,Klipp Edda,Le Chat Ludovic,Lecointe François,Liebermeister Wolfram,March Anika,Noone David,Pohl Susanne,Rinn Bernd,Rügheimer Frank,Samson Franck,Schaffer Marc,Schwikowski Benno,Wiegert Thomas,Devine Kevin M,Wilkinson Anthony J,Bessières Philippe,Noirot Philippe

Date Published: 3rd Mar 2012

Journal: Science

Abstract (Expand)

In Bacillus subtilis the σB mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, ...

Authors: Ulf Liebal, Praveen Kumar Sappa, Thomas Millat, Leif Steil, Uwe Voelker, Olaf Wolkenhauer, Homuth Georg

Date Published: 2012

Journal: Mol. BioSyst.

Abstract (Expand)

Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ-ProA-ProH route is responsible for the production of proline as an osmoprotectant, and the ProB-ProA-ProI route ...

Authors: Tamara Hoffmann, Erhard Bremer, Brill Jeanette,Putzer Harald

Date Published: 13th Jan 2011

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

All regulatory processes require components that sense the environmental or metabolic conditions of the cell, and sophisticated sensory proteins have been studied in great detail. During the last few ...

Authors: Joerg Stuelke, Commichau Fabian M

Date Published: 11th Dec 2007

Journal: Mol. Microbiol.

Abstract:

Not specified

Author: Commichau Fabian M.,Stlke Jrg

Date Published: 16th Dec 2009

Journal: Bacterial Signaling

Abstract (Expand)

Bacteria have developed an impressive ability to survive and propagate in highly diverse and changing environments by evolving phenotypic heterogeneity. Phenotypic heterogeneity ensures that a subpopulation ...

Authors: Imke De Jong, Oscar Kuipers, Haccou Patsy

Date Published: 21st Jan 2011

Journal: Bioessays

Abstract (Expand)

Sortases of Gram-positive bacteria catalyze the covalent C-terminal anchoring of proteins to the cell wall. Bacillus subtilis, a well-known host organism for protein production, contains two putative ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Fasehee Hamidreza,Westers Helga,Bolhuis Albert,Antelmann Haike,Quax Wim J,Mirlohi Agha F,Ahmadian Gholamreza

Date Published: 31st Aug 2011

Journal: Proteomics

Abstract (Expand)

Several computational methods exist to suggest rational genetic interventions that improve the productivity of industrial strains. Nonetheless, these methods are less effective to predict possible ...

Authors: Lope A. Florez, Joerg Stuelke, Gunka Katrin,Polanía Rafael,Tholen Stefan

Date Published: 11th Jan 2011

Journal: BMC Syst Biol

Abstract (Expand)

Systems biology relies increasingly on collaborations between several groups with different expertise. Therefore, the systems biology community is adopting standards that allow effective communication ...

Authors: Lope A. Florez, Joerg Stuelke, Lammers Christoph R,Michna Raphael

Date Published: 14th Oct 2010

Journal: Bioinformatics

Abstract (Expand)

The recent years have seen tremendous progress towards the understanding of microbial metabolism on a higher level of the entire functional system. Hereby, huge achievements including the sequencing ...

Authors: Michael Kohlstedt, Christoph Wittmann, Becker Judith

Date Published: 7th Sep 2010

Journal: Appl. Microbiol. Biotechnol.

Abstract (Expand)

Bacillus subtilis possesses carbon-flux regulating histidine protein (Crh), a paralog of the histidine protein (HPr) of the phosphotransferase system (PTS). Like HPr, Crh becomes (de)phosphorylated in ...

Authors: Wolfgang Hillen, Joerg Stuelke, Landmann Jens J,Werner Susanne,Görke Boris

Date Published: 28th Nov 2011

Journal: FEMS Microbiol. Lett.

Abstract (Expand)

The Bacillus subtilis catabolite control protein A (CcpA) is a global transcriptional regulator which is controlled by interactions with the phosphoproteins HPrSer46P and CrhP and with low molecular ...

Authors: Maike Bartholomae, Uwe Voelker, Gerald Seidel, Wolfgang Hillen, Wünsche Andrea,Hammer Elke,Burkovski Andreas

Date Published: 20th Apr 2012

Journal: The FEBS journal

Abstract (Expand)

The control of mRNA stability is an important component of regulation in bacteria. Processing and degradation of mRNAs are initiated by an endonucleolytic attack, and the cleavage products are processively ...

Authors: Joseph Newman, Rick Lewis, Joerg Stuelke, Lehnik-Habrink Martin,Rothe Fabian M,Solovyova Alexandra S,Rodrigues Cecilia,Herzberg Christina,Commichau Fabian M

Date Published: 29th Jul 2011

Journal: J. Bacteriol.

Abstract (Expand)

RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other ...

Authors: Ulrike Mäder, Joerg Stuelke, Lehnik-Habrink Martin,Schaffer Marc,Diethmaier Christine,Herzberg Christina

Date Published: 4th Aug 2011

Journal: Mol. Microbiol.

Abstract (Expand)

As a versatile pathogen Staphylococcus aureus can cause various disease patterns, which are influenced by strain specific virulence factor repertoires but also by S. aureus physiological adaptation ...

Authors: Uwe Voelker, Michael Hecker, Michael Lalk, Liebeke Manuel,Dörries Kirsten,Zühlke Daniela,Bernhardt Jörg,Fuchs Stephan,Pané-Farré Jan,Engelmann Susanne,Bode Rüdiger,Dandekar Thomas,Lindequist Ulrike

Date Published: 1st Apr 2011

Journal: Mol Biosyst

Abstract (Expand)

SUMMARY: Quinones are highly toxic naturally occurring thiol-reactive compounds. We have previously described novel pathways for quinone detoxification in the Gram-positive bacterium Bacillus subtilis. ...

Authors: Michael Lalk, Michael Hecker, Liebeke Manuel,Pöther Dierk-Christoph,van Duy Nguyen,Albrecht Dirk,Becher Dörte,Hochgräfe Falko,Antelmann Haike

Date Published: 30th Jul 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Twin-arginine protein translocation (Tat) pathways are required for transport of folded proteins across bacterial, archaeal and chloroplast membranes. Recent studies indicate that Tat has evolved into ...

Authors: Ulrike Mäder, Colin Harwood, Michael Hecker, Jan Maarten Van Dijl, van der Ploeg René,Homuth Georg,Schaffer Marc,Denham Emma L,Monteferrante Carmine G,Miethke Marcus,Marahiel Mohamed A,Winter Theresa,Antelmann Haike

Date Published: 30th Mar 2011

Journal: PLoS ONE

Abstract (Expand)

Knowledge on absolute protein concentrations is mandatory for the simulation of biological processes in the context of systems biology. A novel approach for the absolute quantification of proteins at ...

Authors: Sandra Maass, Praveen Kumar Sappa, Uwe Voelker, Michael Hecker, Sievers Susanne,Zühlke Daniela,Kuzinski Judith,Muntel Jan,Hessling Bernd,Bernhardt Jörg,Sietmann Rabea,Becher Dörte

Date Published: 11th Mar 2011

Journal: Anal. Chem.