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The Role of the Nucleoid‐Associated Protein HU in E. coli Transcription
Author(s) -
Bugliosi Sara,
Jessen Erik,
Landick Robert
Publication year - 2016
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.30.1_supplement.1055.10
Subject(s) - nucleoid , rna polymerase , chromatin , transcription (linguistics) , dna , transcription bubble , dna supercoil , biology , rna , microbiology and biotechnology , gene , chemistry , genetics , escherichia coli , dna replication , linguistics , philosophy
Transcription by RNA polymerase (RNAP) is the most basic level by which the cell can regulate gene expression, allowing for dynamic responses to environmental changes. Interactions between RNAP and chromatin‐organizing proteins is one method organisms have evolved to regulate transcription, and is best understood in the context of eukaryotic RNAPs and nucleosomes. In prokaryotes, a set of functionally analogous nucleoid‐associated proteins (NAPs) form interactions with the bacterial chromosome. We are studying how HU, the most abundant NAP in exponentially growing E. coli cells1, coexists on DNA with elongating RNAP. Genome‐scale ChIP data revealed that RNAP and HU are spatially co‐localized along a subset of transcription units (TUs). To investigate why HU was bound only to this subset, additional ChIP experiments against R‐loops were performed. HU has been shown to have high affinity for single‐stranded DNA2. R‐loops are formed upstream of elongation complexes when the nascent RNA transcript invades upstream DNA, displacing a single strand of DNA and making it available for binding by HU. These data showed that whereas R‐loops were exclusively found at TUs bound by HU, deletion of HU had no influence on R‐loop distribution. Analysis of R‐loop‐enriched TU sequences revealed higher G content on the antisense DNA strand and an increased frequency of G‐quartets (GGGG), motifs that have been shown to promote R‐loop formation3. To investigate the physiological significance of these results we tested the viability of an HU deletion strain with an oxygen‐dependent growth defect. We showed that the HU deletion strain is hypersensitive to mutagenic reactive oxygen species (ROSs). Taken together, these results lead us to propose a model in which HU binds to R‐loops upstream of elongating RNAP to protect the exposed non‐template DNA strand from mutagenesis by ROSs.