Publications by authors named "Guenter Raddatz"

7 Publications

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The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.

PLoS One 2011 7;6(10):e24222. Epub 2011 Oct 7.

Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, Essen, Germany.

Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is strictly anaerobic and sulfur-dependent with optimal growth at 86°C and pH 5.6. One particular feature is the great metabolic versatility, which is not accompanied by a distinct increase of genome size or information density as compared to other Crenarchaeota. T. tenax is able to grow chemolithoautotrophically (CO₂/H₂) as well as chemoorganoheterotrophically in presence of various organic substrates. All pathways for synthesizing the 20 proteinogenic amino acids are present. In addition, two presumably complete gene sets for NADH:quinone oxidoreductase (complex I) were identified in the genome and there is evidence that either NADH or reduced ferredoxin might serve as electron donor. Beside the typical archaeal A₀A₁-ATP synthase, a membrane-bound pyrophosphatase is found, which might contribute to energy conservation. Surprisingly, all genes required for dissimilatory sulfate reduction are present, which is confirmed by growth experiments. Mentionable is furthermore, the presence of two proteins (ParA family ATPase, actin-like protein) that might be involved in cell division in Thermoproteales, where the ESCRT system is absent, and of genes involved in genetic competence (DprA, ComF) that is so far unique within Archaea.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024222PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189178PMC
February 2012

The BatR/BatS two-component regulatory system controls the adaptive response of Bartonella henselae during human endothelial cell infection.

J Bacteriol 2010 Jul 23;192(13):3352-67. Epub 2010 Apr 23.

Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.

Here, we report the first comprehensive study of Bartonella henselae gene expression during infection of human endothelial cells. Expression of the main cluster of upregulated genes, comprising the VirB type IV secretion system and its secreted protein substrates, is shown to be under the positive control of the transcriptional regulator BatR. We demonstrate binding of BatR to the promoters of the virB operon and a substrate-encoding gene and provide biochemical evidence that BatR and BatS constitute a functional two-component regulatory system. Moreover, in contrast to the acid-inducible (pH 5.5) homologs ChvG/ChvI of Agrobacterium tumefaciens, BatR/BatS are optimally activated at the physiological pH of blood (pH 7.4). By conservation analysis of the BatR regulon, we show that BatR/BatS are uniquely adapted to upregulate a genus-specific virulence regulon during hemotropic infection in mammals. Thus, we propose that BatR/BatS two-component system homologs represent vertically inherited pH sensors that control the expression of horizontally transmitted gene sets critical for the diverse host-associated life styles of the alphaproteobacteria.
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http://dx.doi.org/10.1128/JB.01676-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897681PMC
July 2010

Mechanisms underlying decoding at 7 T: ocular dominance columns, broad structures, and macroscopic blood vessels in V1 convey information on the stimulated eye.

Neuroimage 2010 Feb 26;49(3):1957-64. Epub 2009 Aug 26.

Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.

Recent studies have demonstrated that multivariate machine learning algorithms applied to human functional MRI data can decode information segregated in cortical columns, despite the voxel size being large relative to the width of columns. The mechanism by which low spatial resolution imaging decodes information represented in a fine-scale organization is not clear. To investigate mechanisms underlying decoding signals we employed high-resolution gradient-echo BOLD functional MRI of visual area V1. We show that in addition to the fine-scale ocular dominance columns, coarse-scale structures extending over several millimeters also convey discriminative power for decoding the stimulated eye. Discriminative power is conveyed by both macroscopic blood vessels and gray matter regions. We hypothesize that gray-matter regions which drain into specific vessels may preferentially contain ocular-dominance columns biased towards one eye; the bias of a specific region thereby causing a functionally selective ocular-dominance response in the associated vessel. Our findings indicate that coarse-scale structures and macroscopic blood vessels contribute to decoding of the stimulated eye based on low-resolution multivariate data.
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http://dx.doi.org/10.1016/j.neuroimage.2009.08.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8485895PMC
February 2010

Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300.

Appl Environ Microbiol 2009 Feb 5;75(3):811-22. Epub 2008 Dec 5.

Mikrobielle Genetik, Eberhard-Karls-Universität Tübingen, Germany.

The Staphylococcus carnosus genome has the highest GC content of all sequenced staphylococcal genomes, with 34.6%, and therefore represents a species that is set apart from S. aureus, S. epidermidis, S. saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs to a family of smaller staphylococcal genomes, and the ori and ter regions are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5 Mbp). The events leading up to this asymmetry probably occurred not that long ago in evolution, as there was not enough time to approach the natural tendency of a physical balance. Unlike the genomes of pathogenic species, the TM300 genome does not contain mobile elements such as plasmids, insertion sequences, transposons, or STAR elements; also, the number of repeat sequences is markedly decreased, suggesting a comparatively high stability of the genome. While most S. aureus genomes contain several prophages and genomic islands, the TM300 genome contains only one prophage, PhiTM300, and one genomic island, nuSCA1, which is characterized by a mosaic structure mainly composed of species-specific genes. Most of the metabolic core pathways are present in the genome. Some open reading frames are truncated, which reflects the nutrient-rich environment of the meat starter culture, making some functions dispensable. The genome is well equipped with all functions necessary for the starter culture, such as nitrate/nitrite reduction, various sugar degradation pathways, two catalases, and nine osmoprotection systems. The genome lacks most of the toxins typical of S. aureus as well as genes involved in biofilm formation, underscoring the nonpathogenic status.
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http://dx.doi.org/10.1128/AEM.01982-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632126PMC
February 2009

Comparative analysis of four Campylobacterales.

Nat Rev Microbiol 2004 Nov;2(11):872-85

Max-Planck-Institute for Developmental Biology, Genome Centre, Spemannstr. 35, 72076 Tübingen, Germany.

Comparative genome analysis can be used to identify species-specific genes and gene clusters, and analysis of these genes can give an insight into the mechanisms involved in a specific bacteria-host interaction. Comparative analysis can also provide important information on the genome dynamics and degree of recombination in a particular species. This article describes the comparative genome analysis of representatives of four different Campylobacterales species - two pathogens of humans, Helicobacter pylori and Campylobacter jejuni, as well as Helicobacter hepaticus, which is associated with liver cancer in rodents, and the non-pathogenic commensal species, Wolinella succinogenes.
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http://dx.doi.org/10.1038/nrmicro1024DOI Listing
November 2004

Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea.

Environ Microbiol 2004 Sep;6(9):970-80

Institute of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.

Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil. In a fosmid end sequencing approach including 5376 sequence tags of approximately 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments (approximately 1% each) have been captured in our libraries. The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured in our libraries, as seen by comparison with sequences in the public databases and by the large variation in G+C contents. We dissect differences between the libraries, which relate to the different ecosystems analysed and to biases introduced by different DNA preparations. Furthermore, a range of taxonomic marker genes (other than 16S rRNA) has been identified that allows the assignment of genome fragments to specific lineages. The complete sequences of two genome fragments identified as being affiliated with Archaea, based on a gene encoding a CDC48 homologue and a thermosome subunit, respectively, are presented and discussed. We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group.
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http://dx.doi.org/10.1111/j.1462-2920.2004.00663.xDOI Listing
September 2004

Complete genome sequence and analysis of Wolinella succinogenes.

Proc Natl Acad Sci U S A 2003 Sep 19;100(20):11690-5. Epub 2003 Sep 19.

Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

To understand the origin and emergence of pathogenic bacteria, knowledge of the genetic inventory from their nonpathogenic relatives is a prerequisite. Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes, which is closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, was determined. Despite being considered nonpathogenic to its bovine host, W. succinogenes holds an extensive repertoire of genes homologous to known bacterial virulence factors. Many of these genes have been acquired by lateral gene transfer, because part of the virulence plasmid pVir and an N-linked glycosylation gene cluster were found to be syntenic between C. jejuni and genomic islands of W. succinogenes. In contrast to other host-adapted bacteria, W. succinogenes does harbor the highest density of bacterial sensor kinases found in any bacterial genome to date, together with an elaborate signaling circuitry of the GGDEF family of proteins. Because the analysis of the W. succinogenes genome also revealed genes related to soil- and plant-associated bacteria such as the nif genes, W. succinogenes may represent a member of the epsilon proteobacteria with a life cycle outside its host.
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http://dx.doi.org/10.1073/pnas.1932838100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC208819PMC
September 2003
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