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Article
Open AccessMGcV: the microbial genomic context viewer for comparative genome analysis
Conserved gene context is used in many types of comparative genome analyses. It is used to provide leads on gene function, to guide the discovery of regulatory sequences, but also to aid in the reconstruction ...
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Article
Open AccessComparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli
The assimilation of nitrogen in bacteria is achieved through only a few metabolic conversions between alpha-ketoglutarate, glutamate and glutamine. The enzymes that catalyze these conversions are glutamine syn...
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Article
Open AccessComparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and ...
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Article
Open AccessAn in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters
T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so...
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Article
Open AccessLocateP: Genome-scale subcellular-location predictor for bacterial proteins
In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a...
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Article
Open AccessA generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1
A key problem in the sequence-based reconstruction of regulatory networks in bacteria is the lack of specificity in operator predictions. The problem is especially prominent in the identification of transcript...
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Article
Open AccessAccelerating the reconstruction of genome-scale metabolic networks
The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinf...
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Article
Flux Control of the Bacterial Phosphoenolpyruvate:Glucose Phosphotransferase System and the Effect of Diffusion
We analyzed the role of diffusion and cell size on the flux control properties of the glucose-PTS of Escherichia coli, in silicon cells under various metabolic conditions. To our surprise, the influence of the co...
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In Vitro Assembly of A “β2 Cytochrome b559” from Chemically Synthesised Peptide
Cytochrome b559 is one of the ubiquitous constituents of the Photosystem II (PSII) reaction centre. Its presence is a prerequisite for the assembly of PSII, but its function is not understood. In contrast to othe...
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Chapter
The Size of the LH1 Antenna of Purple Bacteria
The size of the LH1 antenna of purple bacteria is a matter of dispute. Pigment and protein analyses [1,2] have indicated the presence of 24-27 antenna BChls per reaction center, whereas electron microscopy sug...
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Article
Isolation and pigment composition of the antenna system of four species of green sulfur bacteria
New and rapid procedures were developed for the isolation of chlorosomes and FMO-protein from the green sulfur bacteria Prosthecochloris (P.) aestuarii, Chlorobium (Cb.) phaeovibrioides, Cb. tepidum and Cb. vi...
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Article
Energy transfer from carotenoid and FMO-protein in subcellular preparations from green sulfur bacteria. Spectroscopic characterization of an FMO-reaction center core complex at low temperature
The Fenna-Matthews-Olson (FMO)-protein and the FMO-reaction center (RC) core complex from the green sulfur bacterium Chlorobium tepidum were examined at 6 K by absorption and fluorescence spectroscopy. The absorp...
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Article
The size of the photosynthetic unit in purple bacteria
Pigment analysis was performed by means of normal phase HPLC on a number of bacteriochlorophyll a and b containing species of purple bacteria that contain a core antenna only. At least 99% of the bacteriochloroph...
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Article
Chlorosomes of green sulfur bacteria: Pigment composition and energy transfer
The pigment composition and energy transfer pathways in isolated chlorosomes ofChlorobium phaeovibrioides andChlorobium vibrioforme were studied by means of high performance liquid chromatography (HPLC) and picos...
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Article
Spectroscopic characterization of reaction centers of the (M)Y210W mutant of the photosynthetic bacterium Rhodobacter sphaeroides
The tyrosine-(M)210 of the reaction center of Rhodobacter sphaeroides 2.4.1 has been changed to a tryptophan using site-directed mutagenesis. The reaction center of this mutant has been characterized by low-tempe...
