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Exploring the caulobacter crescentus sos regulon

Apuã César de Miranda Paquola Rodrigo da Silva Galhardo; Carlos Frederico Martins Menck; Congresso do Instituto de Ciências Biomédicas (4. 2005 São Paulo)

Resumos São Paulo: Comissão de Cultura e Extensão Universitária do ICB/USP, 2005

São Paulo Comissão de Cultura e Extensão Universitária do ICB/USP 2005

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  • Título:
    Exploring the caulobacter crescentus sos regulon
  • Autor: Apuã César de Miranda Paquola
  • Rodrigo da Silva Galhardo; Carlos Frederico Martins Menck; Congresso do Instituto de Ciências Biomédicas (4. 2005 São Paulo)
  • Assuntos: MICROBIOLOGIA
  • É parte de: Resumos São Paulo: Comissão de Cultura e Extensão Universitária do ICB/USP, 2005
  • Notas Locais: Disponível somente em CD-ROM
  • Descrição: Introduction and Objectives: Transcriptional regulation is often related to the binding of transcription factors (TFs) to specific sites of DNA (TF binding sites or TFBSs). A prominent example of this type of regulation is the E. coli SOS regulon, which is known to be involved in an "emergency" cell response to extensive damage in DNA and other stress conditions. Caulobacter crescentus is a free living alpha-proteobacterium that emerged as an important model for prokaryotic cell cycle studies. Cell division is asymetric, giving origin to two morphologically distinct daughter cells: one flagellated, motile cell and other, stalked cell. In our work, we searched for a method to define the composition of the SOS regulon of this bacterium. Methods and Results: Using a Gibbs motif sampling algorithm, we obtained a SOS TFBS model from the promoter regions of six genes known to be part of this regulon in E. coli. This motif model was seached in 5' regions of all ORFs of the C. crescentus genome. Among the genes next to the top10 scoring putative TFBSs, we found: lexA, the SOS regulon repressor; the DNA repair genes recA, uvrA, recN and dnaE (catalytic DNA polymerase); and ssb (single strand binding protein). Conclusion: With the adopted score cutoff, we were able to capture 68% of the known E. coli SOS boxes with an estimated true positive rate of 72%. Extrapolating this argument to Caulobacter crescentus genome, we could expect that about 2/3 of predicted TFBSs with the
    same score cutoff would correspond to true LexA binding sites
  • Editor: São Paulo Comissão de Cultura e Extensão Universitária do ICB/USP
  • Data de criação/publicação: 2005
  • Formato: res. 29.
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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