Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response

Authors

Deepak Balasubramania, Department of Biological Sciences, Florida International UniversityFollow
Hansi Kumari, Herbert Wertheim College of Medicine, Florida International UniversityFollow
Melita Jaric, Bioinformatics Research Group, Florida International University
Mitch Fernandez, Bioinformatics Research Group, Florida International University
Keith H. Turner, Harvard Medical School
Simon L. Dove, Harvard Medical School
Giri Narasimhan, Bioinformatics Research Group, Florida International UniversityFollow
Stephen Lory, Harvard Medical School
Kalai Mathee, Herbert Wertheim College of Medicine, Florida International UniversityFollow

Date of this Version

10-2013

Document Type

Article

Abstract

Pathogenicity of Pseudomonas aeruginosa, a major cause of many acute and chronic human infections, is determined by tightly regulated expression of multiple virulence factors. Quorum sensing (QS) controls expression of many of these pathogenic determinants. Previous microarray studies have shown that the AmpC β-lactamase regulator AmpR, a member of the LysR family of transcription factors, also controls non-β-lactam resistance and multiple virulence mechanisms. Using RNA-Seq and complementary assays, this study further expands the AmpR regulon to include diverse processes such as oxidative stress, heat shock and iron uptake. Importantly, AmpR affects many of these phenotypes, in part, by regulating expression of non-coding RNAs such as rgP32, asRgsA, asPrrF1 and rgRsmZ. AmpR positively regulates expression of the major QS regulators LasR, RhlR and MvfR, and genes of the Pseudomonas quinolone system. Chromatin immunoprecipitation (ChIP)-Seq and ChIP–quantitative real-time polymerase chain reaction studies show that AmpR binds to the ampC promoter both in the absence and presence of β-lactams. In addition, AmpR directly binds the lasR promoter, encoding the QS master regulator. Comparison of the AmpR-binding sequences from the transcriptome and ChIP-Seq analyses identified an AT-rich consensus-binding motif. This study further attests to the role of AmpR in regulating virulence and physiological processes in P. aeruginosa.

Comments

Originally published in Nucleic Acids Research.

Identifier

FIDC008521

Recommended Citation

Balasubramania, Deepak; Kumari, Hansi; Jaric, Melita; Fernandez, Mitch; Turner, Keith H.; Dove, Simon L.; Narasimhan, Giri; Lory, Stephen; and Mathee, Kalai, "Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response" (2013). HWCOM Faculty Publications. 196.
https://digitalcommons.fiu.edu/com_facpub/196

Creative Commons License

This work is licensed under a Creative Commons Attribution 3.0 License.