PMID:24157832

Citation	Balasubramanian, D, Kumari, H, Jaric, M, Fernandez, M, Turner, KH, Dove, SL, Narasimhan, G, Lory, S and Mathee, K' (2013) Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response. Nucleic Acids Res. '
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.
Links	PubMed Online version:10.1093/nar/gkt942
Keywords
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
PSEAE:LASR	NOT	GO:0016563: transcription activator activity	ECO:0000314:		F		Figure 8. AmpR positively regulates critical QS regulators of the Las system, Rhl system and PQS. Expression of the genes was determined by qPCR.	complete CACAO 8937
PSEAE:AMPR	NOT	GO:0030528: transcription regulator activity	ECO:0000314:		F		Figure 5 Regulation of heat-shock response by AmpR.	complete CACAO 8936
PSEAE:AMPR	part_of	GO:0032993: protein-DNA complex	ECO:0005620: chromatin immunoprecipitation-PCR evidence used in manual assertion		C		Seeded From UniProt	complete
PSEAE:AMPR	part_of	GO:0032993: protein-DNA complex	ECO:0006009: chromatin immunoprecipitation-seq evidence used in manual assertion		C		Seeded From UniProt	complete
PSEAE:AMPR	enables	GO:0043565: sequence-specific DNA binding	ECO:0005620: chromatin immunoprecipitation-PCR evidence used in manual assertion		F		Seeded From UniProt	complete
PSEAE:AMPR	enables	GO:0043565: sequence-specific DNA binding	ECO:0006009: chromatin immunoprecipitation-seq evidence used in manual assertion		F		Seeded From UniProt	complete
PSEAE:RHLB	NOT	GO:0004004: ATP-dependent RNA helicase activity	ECO:0000314:		F		AmpR positively regulates critical QS regulators of the Las system, Rhl system and PQS. Expression of the genes was determined by qPCR.	complete CACAO 8938
PSEAE:Q9I4X0	NOT	GO:0030528: transcription regulator activity	ECO:0000314:		F		AmpR positively regulates critical QS regulators of the Las system, Rhl system and PQS. Expression of the genes was determined by qPCR.	complete CACAO 8939

References

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