High-resolution RNA 3'-ends mapping of bacterial Rho-dependent transcripts.
Nucleic Acids Res
; 46(13): 6797-6805, 2018 07 27.
Article
in En
| MEDLINE
| ID: mdl-29669055
ABSTRACT
Transcription termination in bacteria can occur either via Rho-dependent or independent (intrinsic) mechanisms. Intrinsic terminators are composed of a stem-loop RNA structure followed by a uridine stretch and are known to terminate in a precise manner. In contrast, Rho-dependent terminators have more loosely defined characteristics and are thought to terminate in a diffuse manner. While transcripts ending in an intrinsic terminator are protected from 3'-5' exonuclease digestion due to the stem-loop structure of the terminator, it remains unclear what protects Rho-dependent transcripts from being degraded. In this study, we mapped the exact steady-state RNA 3' ends of hundreds of Escherichia coli genes terminated either by Rho-dependent or independent mechanisms. We found that transcripts generated from Rho-dependent termination have precise 3'-ends at steady state. These termini were localized immediately downstream of energetically stable stem-loop structures, which were not followed by uridine rich sequences. We provide evidence that these structures protect Rho-dependent transcripts from 3'-5' exonucleases such as PNPase and RNase II, and present data localizing the Rho-utilization (rut) sites immediately downstream of these protective structures. This study represents the first extensive in-vivo map of exact RNA 3'-ends of Rho-dependent transcripts in E. coli.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
RNA, Messenger
/
Terminator Regions, Genetic
/
Escherichia coli Proteins
/
Escherichia coli
/
Transcription Termination, Genetic
Language:
En
Journal:
Nucleic Acids Res
Year:
2018
Type:
Article
Affiliation country:
Israel