MiST: a microbial signal transduction database

Signal transduction pathways control most cellular activities in living cells ranging from regulation of gene expression to fine-tuning enzymatic activity and controlling motile behavior in response to extracellular and intracellular signals. Because of their extreme sequence variability and extensive domain shuffling, signal transduction proteins are difficult to identify, and their current annotation in most leading databases is often incomplete or erroneous. To overcome this problem, we have developed the microbial signal transduction (MiST) database (), a comprehensive library of the signal transduction proteins from completely sequenced bacterial and archaeal genomes. By searching for domain profiles that implicate a particular protein as participating in signal transduction, we have systematically identified 69 270 two- and one-component proteins in 365 bacterial and archaeal genomes. We have designed a user-friendly website to access and browse the predicted signal transduction proteins within various organisms. Further capabilities include gene/protein sequence retrieval, visualized domain architectures, interactive chromosomal views for exploring gene neighborhood, advanced querying options and cross-species comparison. Newly available, complete genomes are loaded into the database each month. MiST is the only comprehensive and up-to-date electronic catalog of the signaling machinery in microbial genomes

MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. Newsoftware infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes

MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. New software infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes. The data can be explored online or via RESTful API (freely available at https://mistdb.com)

The XX-model with boundaries. Part III:Magnetization profiles and boundary bound states

We calculate the magnetization profiles of the $\sigma_j^x$ and $\sigma_j^z$ operators for the XX-model with hermitian boundary terms. We study the profiles on the finite chain and in the continuum limit. The results are discussed in the context of conformal invariance. We also discuss boundary excitations and their effect on the magnetization profiles.Comment: 30 pages, 3 figure

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

The Mass Definition in Hqet and a New Determination of Vcb_{\text{cb}}

Positive powers of the mass parameter in a physical quantity calculated with the help of heavy quark effective theory originate from a Wilson coefficient in the matching of QCD and HQET Green function. We show that this mass parameter enters the calculation as a well--defined running current mass. We further argue that the recently found ill--definition of the pole mass, which is the natural expansion parameter of HQET, does not affect a phenomenological analysis which uses truncated perturbative series. We reanalyse inclusive semileptonic decays of heavy mesons and obtain the $c$ quark mass $m_c^{\overline{\text{MS}}}(m_c) = (1.35\pm 0.20)\,\text{GeV}$ where the error is almost entirely due to scale--uncertainties. We also obtain $m_b^{\overline{\text{MS}}}(m_b) = (4.6\pm 0.3)\,\text{GeV}$ and $|V_{cb}|(\tau_B/1.49\,\text{ps})^{1/2} = 0.036\pm 0.005$ where the errors come from the uncertainty in the kinetic energy of the heavy quark inside the meson, in the experimental branching ratios, in QCD input parameters, and scale--uncertainties.Comment: 21 p., 5 figs, all style files incl., TUM-T31-56/R (Sec. 2 revised, phenomenological results unchanged

The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota

<p>Abstract</p> <p>Background</p> <p><it>Staphylothermus marinus </it>is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes.</p> <p>Results</p> <p>The 1.57 Mbp genome of the hyperthermophilic crenarchaeote <it>Staphylothermus marinus </it>has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. <it>S. marinus </it>possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. <it>S. marinus </it>lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced – <it>Thermofilum pendens </it>and <it>Hyperthermus butylicus</it>. Instead it has three operons similar to the <it>mbh </it>and <it>mbx </it>operons of <it>Pyrococcus furiosus</it>, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, <it>S. marinus </it>and <it>H. butylicus</it>, possess more sodium-dependent transporters than <it>T. pendens </it>and use symporters for potassium uptake while <it>T. pendens </it>uses an ATP-dependent potassium transporter. <it>T. pendens </it>has adapted to a nutrient-rich environment while <it>H. butylicus </it>is adapted to a nutrient-poor environment, and <it>S. marinus </it>lies between these two extremes.</p> <p>Conclusion</p> <p>The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.</p

Comparative chromosome painting discloses homologous Segments in distantly related mammals

Comparative chromosome painting, termed ZOO-FISH, using DNA libraries from flow sorted human chromosomes 1,16,17 and X, and mouse chromosome 11 discloses the presence of syntenic groups in distantly related mammalian Orders ranging from primates (Homo sapiens), rodents (Mus musculus), even-toed ungulates (Muntiacus muntjak vaginalis and Muntiacus reevesi) and whales (Balaenoptera physalus). These mammalian Orders have evolved separately for 55-80 million years (Myr). We conclude that ZOO-FISH can be used to generate comparative chromosome maps of a large number of mammalian species