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E-GEOD-77748 - An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [RNA-Seq]

Status
Released on 7 July 2016, last updated on 9 July 2016
Organism
Streptococcus pneumoniae R6
Samples (6)
Protocols (3)
Description
We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. Likewise, recovery of viability and DNA-supercoiling were observed when cells were treated with those SCN concentrations and the drug was removed. The main DNA topoisomerase gene affected was topA, whose transcription depended on the supercoiling level. A two stage global transcriptomic response with 8 µM seconeolitsine was detected. The early stage (5 and 15 min, 10% of the genome) represented a response induced by increased supercoiling. The second stage represented supercoiling recovery (30 min, 2.0% of the genome). Almost 25% of the early responsive genes formed clusters with coordinated transcriptional regulation. Twelve clusters were evident, with sizes of 6.7 to 31.4 Kb (9 to 22 responsive genes). Strikingly, clusters did not contradict those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using overlapping responses. This is the first study describing a global transcriptomic response triggered by an increase in DNA supercoiling in bacteria. Total RNA was extracted from S. pneumoniae R6 cultures during exponential growth and used for RNA-Seq. Two independent replicates per condition were performed.
Experiment type
RNA-seq of coding RNA 
Contacts
Antonio J. Martin-Galiano <mgaliano@isciii.es>, Adela G de la Campa, Antonio J Martin-Galiano, María J Ferrándiz
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-77748.idf.txt
Sample and data relationshipE-GEOD-77748.sdrf.txt
Processed data (1)E-GEOD-77748.processed.1.zip
Links