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| Status |
Public on Jul 08, 2019 |
| Title |
Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
In many gram-negative and some gram-positive bacteria small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism, and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. Here, we report that PNPase uniquely contributes to the degradation of specific mRNA cleavage products, the majority of which bind Hfq and are derived from targets of sRNAs. Specifically, we found that these mRNA-derived fragments accumulate in the absence of PNPase or its exoribonuclease activity and interact with PNPase. Additionally, we show that mutations in hfq or in the seed pairing region of a sRNA eliminated the requirement of PNPase for sRNA stability. Altogether, our results are consistent with a model that PNPase degrades mRNA-derived fragments that could otherwise deplete cells of Hfq-binding sRNAs through pairing mediated decay.
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| Overall design |
Examination of mRNA expression in four samples of strains carrying wild type or mutant genes of rph and/or pnp. Additional examination of four samples from pnp wild type and mutant strains of RNA from Hfq co-immunoprecipitation input and output fractions. All samples were sequenced with two biological replicates.
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| Contributor(s) |
De Lay NR |
| Citation(s) |
31329973 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM121368 |
Systematic analysis of small RNA-based regulation of gene expression in bacteria |
UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON |
Nicholas R. De Lay |
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| |
| Submission date |
Jan 18, 2019 |
| Last update date |
Oct 07, 2019 |
| Contact name |
Nicholas De Lay |
| E-mail(s) |
nicholas.r.delay@uth.tmc.edu
|
| Phone |
713-500-6293
|
| Organization name |
University of Texas Health Science Center
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
6431 Fannin St
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL15010 |
Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA515929 |
| SRA |
SRP180336 |
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