Topo-Club 2016

Effects of genome position of supercoiling-dependent gene expression

Non programmé

15m

Salle François Jacob (Institut Jacques Monod)

Orateur

Dr Bianca Sclavi (LBPA, UMR 8113)

Description

Global transcription regulators are factors that can influence the activity of several bacterial promoters and can thus play a key role during bacterial adaptation to a change in growth environment. These factors include small metabolites, such as ppGpp, abundant nucleoid-associated proteins and DNA topology. The latter two are not equally repartitioned throughout the genome and could thus influence gene expression differently depending on the gene's position along the genome (1,2,3). Our previous work provided evidence for a genome-position dependence of the activity of an H-NS dependent promoter (4). This effect became particularly evident when gene expression was compared as a function of growth rate, growth phase or temperature. Recently we have begun studying the activity of supercoiling-dependent promoters in order to determine whether the effects of DNA topology also depend on genomic position, as suggested by existing data on the binding sites of topoisomerases (5). In this study we have found both local and global effects of genomic position on a supercoiling-dependent promoter, furthermore our results show that the activity of nucleoid proteins can either buffer or amplify these effects depending on the genomic context. 1.Sobetzko, P., Glinkowska, M., Travers, A., and Muskhelishvili, G. (2013). DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle. Mol Biosyst 9, 1643–1651. 2. Scolari, V.F., Bassetti, B., Sclavi, B., Cosentino Lagomarsino, M. (2010) Gene clusters reflecting macrodomain structure respond to nucleoid perturbations. Molecular BioSystems, DOI: 10.1039/C0MB00213E. 3. Zarei, M., Sclavi,B. Cosentino Lagomarsino, M. (2013) Gene silencing and large-scale domain structure of the E. coli genome, Mol. BioSyst., 2013, 9 (4), 758 - 767 4. Brambilla, E. and Sclavi, B. (2015) Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in E. coli. G3, Genes, Genomes, Genomics, 5, 605-614. 5.Jeong, K.S., Ahn, J., and Khodursky, A.B. (2004). Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol. 5, R86.