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DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium
Author(s) -
Booker Betty M.,
Deng Shuang,
Higgins N. Patrick
Publication year - 2010
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/j.1365-2958.2010.07394.x
Subject(s) - dna supercoil , dna gyrase , operon , transcription (linguistics) , biology , nucleoid , rna polymerase , dna , tn3 transposon , gene , genetics , microbiology and biotechnology , rna , escherichia coli , dna replication , transposable element , genome , linguistics , philosophy
Summary Bacteria differ from eukaryotes by having the enzyme DNA gyrase, which catalyses the ATP‐dependent negative supercoiling of DNA. Negative supercoils are essential for condensing chromosomes into an interwound (plectonemic) and branched structure known as the nucleoid. Topo‐1 removes excess supercoiling in an ATP‐independent reaction and works with gyrase to establish a topological equilibrium where supercoils move within 10 kb domains bounded by stochastic barriers along the sequence. However, transcription changes the stochastic pattern by generating supercoil diffusion barriers near the sites of gene expression. Using supercoil‐dependent Tn 3 and γδ resolution assays, we studied DNA topology upstream, downstream and across highly transcribed operons. Whenever two Res sites flanked efficiently transcribed genes, resolution was inhibited and the loss in recombination efficiency was proportional to transcription level. Ribosomal RNA operons have the highest transcription rates, and resolution assays at the rrnG and rrnH operons showed inhibitory levels 40–100 times those measured in low‐transcription zones. Yet, immediately upstream and downstream of RNA polymerase (RNAP) initiation and termination sites, supercoiling characteristics were similar to poorly transcribed zones. We present a model that explains why RNAP blocks plectonemic supercoil movement in the transcribed track and suggests how gyrase and TopA control upstream and downstream transcription‐driven supercoiling.