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PMID:24708042

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Citation

Vakulskas, CA, Pannuri, A, Cortés-Selva, D, Zere, TR, Ahmer, BM, Babitzke, P and Romeo, T (2014) Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures. Mol. Microbiol. 92:945-58

Abstract

In Escherichia coli, activity of the global regulatory RNA binding protein CsrA is antagonized by two non-coding sRNAs, CsrB and CsrC, which sequester it away from its lower affinity mRNA targets. Transcription of csrB/C requires the BarA-UvrY two component signal transduction system, which responds to short chain carboxylates. We show that two DEAD-box RNA helicases, DeaD and SrmB, activate csrB/C expression by different pathways. DeaD facilitates uvrY translation by counteracting the inhibitory effect of long distance base-pairing between the uvrY mRNA leader and coding region, while SrmB does not affect UvrY or UvrY-phosphate levels. Contrary to the prevailing notion that these helicases act primarily at low temperatures, DeaD and SrmB activated csrB expression over a wide temperature range. High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) revealed in vivo interactions of DeaD with 39 mRNAs, including those of uvrY and 9 other regulatory genes. Studies on the expression of several of the identified genes revealed regulatory effects of DeaD in all cases and diverse temperature response patterns. Our findings uncover an expanded regulatory role for DeaD, which is mediated through novel mRNA targets, important global regulators and under physiological conditions that were considered to be incompatible with its function.

Links

PubMed PMC4048959 Online version:10.1111/mmi.12606

Keywords

DEAD-box RNA Helicases/genetics; DEAD-box RNA Helicases/metabolism; Gene Expression Regulation, Bacterial/genetics; Gene Expression Regulation, Bacterial/physiology; RNA, Messenger/genetics; Temperature

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

ECOLI:DEAD

acts_upstream_of_or_within

GO:0045727: positive regulation of translation

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ECOLI:DEAD

involved_in

GO:0045727: positive regulation of translation

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

Notes

See also

References

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