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

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

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

Date Published: 2010

Journal: Not specified

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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, The STREAM Consortium (stream), David Hodgson, Elizabeth Wellington, Eriko Takano, Rainer Breitling

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

Date Published: 28th May 2009

Journal: BMC Genomics

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

Date Published: 2nd May 2008

Journal: PLoS ONE

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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: Nai-Hua Hsiao, Marco Gottelt, Eriko Takano

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, Dennis Vitkup, Michael P Barrett

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

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

Date Published: 18th Dec 2008

Journal: Bioinformatics

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

Date Published: 22nd Oct 2008

Journal: Proteomics

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

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, Alberto Sola-Landa, Kristian Apel, Fernando Santos-Beneit, Juan-Francisco Martin

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

Date Published: 1st Apr 2009

Journal: Microbiology (Reading, Engl.)

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

Date Published: 7th Jan 2008

Journal: Mol. Microbiol.

Abstract:

Not specified

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

Date Published: 9th Apr 2008

Journal: Adv. Appl. Microbiol.

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

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

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, Jannis Uhlendorf, Timo Lubitz, Marvin Schulz, Edda Klipp, Wolfram Liebermeister

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, José L Martínez, Jaromir Zahrádka, Joaquin Ariño, Hana Sychrova, Jose Ramos

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

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

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

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

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, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig

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, Adrian J Koerber, Paul Williams

Date Published: 19th Feb 2009

Journal: J Math Biol

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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, Paul Williams

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

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

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

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, Zhian Saleihan, Ingolf Nes, Helge Holo

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

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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, Paul A M Michels, Rainer Breitling, Mike Barrett

Date Published: 6th May 2010

Journal: Parasitology

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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

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

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

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

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

Date Published: 16th Jan 2008

Journal: Mol. Microbiol.

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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: Haike Antelmann, Michael Hecker, Peter Zuber

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

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

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

Date Published: 21st May 2008

Journal: Proteomics

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

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: Boris Görke, Joerg Stuelke

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, Haike Antelmann, Knut Büttner, Jörg Bernhardt

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

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: Thijs R H M Kouwen, Jan Maarten Van Dijl

Date Published: 30th May 2008

Journal: Trends Microbiol.

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

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, Sree N Sreenath, Radina P Soebiyanto, Jayant Avva, Kwang-Hyun Cho, Olaf Wolkenhauer

Date Published: 17th Jan 2007

Journal: BioSystems

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

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

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

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

Date Published: 2nd Dec 2007

Journal: Microb. Cell Fact.

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

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

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

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

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

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

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

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, Sebastian F Roppel, Arne G Schmeisky, Christoph R Lammers, Joerg Stuelke

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

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: Thijs R H M Kouwen, Jan Maarten Van Dijl

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

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

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: Manuel Liebeke, Ariane Wunder, Michael Lalk

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

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

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

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

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

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, Alexander Reder, Stephan Fuchs, Martin Pagels, Susanne Engelmann

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

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

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

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, Jan-Hendrik S. Hofmeyr

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, Birgit Voigt, Michael Hecker, Hubert Bahl, Ralf-Jörg Fischer

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

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

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, Anja Pritzschke, Nikolai Siemens, Ingolf Nes, Jeroen Hugenholtz, Bernd Kreikemeyer

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.

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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, Eleanor W Trotter, H M Shahzad Asif, Guido Sanguinetti, Joost Teixeira De Mattos, Robert Poole, Jeff Green

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, Venelina Sugareva, Nadja Patenge, Bernd Kreikemeyer

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, Aleksandra Bochkareva, Vasisht R Tadigotla, Mohammad Roghanian, Savva Zorov, Konstantin Severinov, Nikolay Zenkin

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: Graham Scholefield, Jan-Willem Veening, Heath Murray

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

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

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, Heath Murray, Jeff Errington

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: Mohammad Roghanian, Yulia Yuzenkova, Nikolay Zenkin

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, Ellen M Fergestad, Geir Mathiesen, Ingolf Nes, Helge Holo

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: Yulia Yuzenkova, Nikolay Zenkin

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: Marta Łuksza, Michael Lässig, Johannes Berg

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

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, Dominik Esser, Susanne Gertig, Patrick Haferkamp, Theresa Kouril, Andrea Manica, Trong Khoa Pham, Julia Reimann, Kerstin Schreiber, Pawel Sierocinski, Daniela Teichmann, Marleen van Wolferen, 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

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

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

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

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, Geert Van Den Bogaart, Liesbeth Veenhoff, Victor Krasnikov, Bert Poolman

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

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: Jan Spitzer, Bert Poolman

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

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

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

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, Katrin Beilharz, Oscar Kuipers, Jan-Willem Veening

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, Ellen M Faergestad, Martijn Bekker, Lars Snipen, Ingolf Nes, Helge Holo

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, Vasisht R Tadigotla, Konstantin Severinov, Nikolay Zenkin

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

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: Daniel Castro-Roa, Nikolay Zenkin

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

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

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, Matthew Horridge, Olga Krebs, Wolfgang Müller, Jacky Snoep, Franco Du Preez, Carole Goble

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

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

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

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

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, Christian Bock

Date Published: 1st Feb 2010

Journal: Analytical Biochemistry

Abstract:

Not specified

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

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, Christina Grimmler, Armin Ehrenreich, Servé Kengen

Date Published: 1st Mar 2012

Journal: Journal of Biotechnology

Abstract:

Not specified

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

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

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, Georg Homuth, Uwe Voelker, Olaf Wolkenhauer

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

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: Fabian M Commichau, Joerg Stuelke

Date Published: 11th Dec 2007

Journal: Mol. Microbiol.

Abstract:

Not specified

Authors: Fabian M. Commichau, Jrg Stlke

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, Patsy Haccou, Oscar Kuipers

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

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, Katrin Gunka, Rafael Polanía, Stefan Tholen, Joerg Stuelke

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, Christoph R Lammers, Raphael Michna, Joerg Stuelke

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, Judith Becker, Christoph Wittmann

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

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

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

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

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

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

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

Date Published: 30th Mar 2011

Journal: PLoS ONE