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A study into sigma-54 regulated genes

A study into sigma-54 regulated genes. Bamics meeting October 17, 2011. Tom Groot Kormelink Rob Vogels Christof Francke. A study into the sigma-54 regulated genes and operons in 6 Bacillus Anthracis , 9 Bacillus Cereus and 3 Bacillus Thuringiensis species.

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A study into sigma-54 regulated genes

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  1. A study into sigma-54 regulated genes Bamics meeting October 17, 2011 Tom Groot Kormelink Rob Vogels Christof Francke

  2. A study into the sigma-54 regulated genes and operons in 6 Bacillus Anthracis,9 Bacillus Cereus and 3 Bacillus Thuringiensis species * Analysis of the sigma-54 regulon * Identification of different types of EBPs

  3. A study into the sigma-54 regulated genes and operons in 6 Bacillus Anthracis,9 Bacillus Cereus and 3 Bacillus Thuringiensis species * Analysis of the sigma-54 regulon: same Problem of analysis by student: we do not know if the gene is present in the genome, we only know there is no s54 promoter found

  4. A study into the sigma-54 regulated genes and operons in 6 Bacillus Anthracis,9 Bacillus Cereus and 3 Bacillus Thuringiensis species * 8 Different types of EBPs in the 19 Bacillus species:

  5. A study into the sigma-54 regulated genes and operons in 6 Bacillus Anthracis,9 Bacillus Cereus and 3 Bacillus Thuringiensis species * 8 Different types of EBPs in the 19 Bacillus species: * AAA domain is necessary for sigma-54 remodeling * HTH8 domain that functions as a DNA binding motif * PAS domain used as a signal sensor * GAF is involved with many different small signaling molecules * PRD and EII domains are phosphorylatable domains involved in PTS regulation No TCS associated EBPs!

  6. A study into the sigma-54 regulated genes and operons in 6 Bacillus Anthracis,9 Bacillus Cereus and 3 Bacillus Thuringiensis species * 8 Different types of EBPs in the 19 Bacillus species:

  7. Sub-regulon prediction So the sigma-54 regulon actually consists of several sub-regulons, where each one is activated by different input signals. Predict sub-regulons: search for the Upstream Activating Sequences

  8. Sig-54 present in sporulating Firmicutes, not in other LPS- bacteria * Link to sporulation? * Acetonema longum: The inner membrane of the mother cell becomes the outer membrane of the germinating cell. * Surface of outgrowing cells: LPS, carbohydrate components, glycosyl, beta-hydroxy fatty acids

  9. PTS-related EBP Predicted sigma54 dependent promoter One of the best-scoring: 96% EBP Gene missed Inactive?

  10. BS_mnaA Identification of an essential gene of Listeria monocytogenes involved in teichoic acid biogenesis. Dubail I, Bigot A, Lazarevic V, Soldo B, Euphrasie D, Dupuis M, Charbit A. J Bacteriol. 2006 Sep;188(18):6580-91. Annotation of these systems requires work Can not be based on BLAST BS_tagO Characterization of a Bacillus subtilis thermosensitive teichoic acid-deficient mutant: gene mnaA (yvyH) encodes the UDP-N-acetylglucosamine 2-epimerase. Soldo B, Lazarevic V, Pooley HM, Karamata D. J Bacteriol. 2002 Aug;184(15):4316-20. tagO is involved in the synthesis of all anionic cell-wall polymers in Bacillus subtilis 168. Soldo B, Lazarevic V, Karamata D. Microbiology. 2002 Jul;148(Pt 7):2079-87. BS_ywqF How tyrosine phosphorylation affects the UDP-glucose dehydrogenase activity of Bacillus subtilis YwqF. Mijakovic I, Petranovic D, Deutscher J. J Mol Microbiol Biotechnol. 2004;8(1):19-25.

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