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#supercoiling

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Transcription in Prokaryotes

Negative supercoils behind RNA polymerase are removed by

Behind elongating RNA polymerase, DNA becomes transiently underwound creating negative supercoiling that favors strand separation and R-loop formation where nascent RNA anneals to template strand displacing non-template strand. Type IA topoisomerase I encoded by topA in E. coli cleaves single strand of duplex without ATP, allows passage of other strand through break, then religates, incrementally relaxing negative supercoils. Activity restores normal superhelical density behind complex, preventing excessive unwinding that would promote genome instability. DNA gyrase acts ahead removing positive supercoils; distinct substrate preferences ensure topological homeostasis balanced during active transcription and replication.

Ref: Berg Biochemistry Section 6.3: Topoisomerase I removes negative supercoils behind polymerase; Alberts Chapter 5: Topo I role transcription trailing domain

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Transcription in Prokaryotes

During elongation, positive supercoils ahead of RNA polymerase are removed by

Transcription induces twin supercoiled domains because elongating polymerase cannot freely rotate around DNA helix. Positive overwound supercoils accumulate ahead of polymerase creating torsional stress opposing unwinding, while negative underwound supercoils trail behind. DNA gyrase, a type IIA topoisomerase unique to bacteria introducing negative supercoils using ATP-driven double-strand passage, preferentially removes positive supercoils in front of transcription complex. Topoisomerase IV also contributes chromosome decatenation. Topo I handles negative behind. This division of labor ensures polymerase advancement unimpeded by excessive supercoiling accumulation that would otherwise stall elongation or promote R-loop formation.

Ref: Watson Molecular Biology Gene 7th ed. Chapter 4: Gyrase removes positive supercoils ahead RNAP; Alberts Chapter 5 Supercoiling transcription domains

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