E. coli Fis Protein Insulates the cbpA Gene from Uncontrolled Transcription

Chintakayala, Kiran; Singh, Shivani; Rossiter, Amanda E.; Shahapure, Rajesh; Dame, Remus T.; Grainger, David C.

doi:10.1371/journal.pgen.1003152

Cited by 33 publications

(28 citation statements)

References 42 publications

(50 reference statements)

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“…B. i) Stimulation of P ehxCABD by H-NS in vitro . The figure shows the results of an in vitro transcription reaction calibrated with transcripts of known size from the cbpA regulatory region [35]. The 178 nt transcript initiates from P ehxCABD and the 108 nt RNAI transcript is an internal control.…”

Section: Resultsmentioning

confidence: 99%

H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

Singh

Grainger

2013

PLoS Genet

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Extremely AT-rich DNA sequences present a challenging template for specific recognition by RNA polymerase. In bacteria, this is because the promoter −10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions. Thus, at the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter −10 element and similar overlapping sequences. This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. Our work provides mechanistic insight into nucleoprotein structure and its effect on protein-DNA interactions in prokaryotic cells.

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Section: Resultsmentioning

confidence: 99%

H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

Singh

Grainger

2013

PLoS Genet

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“…In growing cells, Fis and H-NS work together to repress the transcription of dps (Grainger et al 2008). Fis also represses cbpA transcription (Chintakayala et al 2013). When IHF, HU, H-NS, and Fis levels fall, the nucleoid becomes compacted by Dps (Akerlund et al 1995).…”

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confidence: 99%

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

et al. 2015

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The mutagenicity of DNA double-strand break repair in Escherichia coli is controlled by DNA-damage (SOS) and general (RpoS) stress responses, which let error-prone DNA polymerases participate, potentially accelerating evolution during stress. Either base substitutions and indels or genome rearrangements result. Here we discovered that most small basic proteins that compact the genome, nucleoid-associated proteins (NAPs), promote or inhibit mutagenic break repair (MBR) via different routes. Of 15 NAPs, H-NS, Fis, CspE, and CbpA were required for MBR; Dps inhibited MBR; StpA and Hha did neither; and five others were characterized previously. Three essential genes were not tested. Using multiple tests, we found the following: First, Dps, which reduces reactive oxygen species (ROS), inhibited MBR, implicating ROS in MBR. Second, CbpA promoted F9 plasmid maintenance, allowing MBR to be measured in an F9-based assay. Third, Fis was required for activation of the SOS DNA-damage response and could be substituted in MBR by SOS-induced levels of DinB error-prone DNA polymerase. Thus, Fis promoted MBR by allowing SOS activation. Fourth, H-NS represses ROS detoxifier sodB and was substituted in MBR by deletion of sodB, which was not otherwise mutagenic. We conclude that normal ROS levels promote MBR and that H-NS promotes MBR by maintaining ROS. CspE positively regulates RpoS, which is required for MBR. Four of five previously characterized NAPs promoted stress responses that enhance MBR. Hence, most NAPs affect MBR, the majority via regulatory functions. The data show that a total of six NAPs promote MBR by regulating stress responses, indicating the importance of nucleoid structure and function to the regulation of MBR and of coupling mutagenesis to stress, creating genetic diversity responsively.

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“…This would likely impose a fitness cost, since de-repression of H-NSsilenced intragenic promoters diverts RNAP away from housekeeping genes (Lamberte et al, 2017). It may also impact the expression of neighbouring genes, since H-NS-silenced promoters within genes can potentially transcribe mRNAs for downstream genes (Chintakayala et al, 2013;Lamberte et al, 2017).…”

Section: Implications For Genome Evolutionmentioning

confidence: 99%

Waking the neighbours: disruption of H‐NS repression by overlapping transcription

Wade

Grainger

2018

Molecular Microbiology

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The histone-like nucleoid structuring (H-NS) protein and its analogues bind large stretches of horizontally acquired AT-rich DNA in a broad range of bacterial species. Binding by H-NS silences the promoters within such DNA that would otherwise deplete the cellular pool of RNA polymerase. Selective de-repression can occur when sequence-specific DNA-binding proteins locally disrupt H-NS function; this mechanism is important for the regulation of many virulence genes. In this issue of Molecular Microbiology, Rangarajan and Schnetz show that when transcription from a neighbouring region invades an H-NS-bound locus, it can disrupt local H-NS repression. Moreover, they show that de-repression occurs in a dose-dependent manner, and they demonstrate a natural example of this in Escherichia coli. This finding has important implications for H-NS function and its impact on genome evolution.

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E. coli Fis Protein Insulates the cbpA Gene from Uncontrolled Transcription

Cited by 33 publications

References 42 publications

H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

Waking the neighbours: disruption of H‐NS repression by overlapping transcription

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