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Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA.

Abstract：

:Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison revealed in 45 antisense RNA control systems a 5' YUNR motif indicative for the formation of a U-turn structure in either an antisense or a target RNA loop and confirmed in the case of the hok/sok system of plasmid R1 its importance for regulation.Here, we demonstrate the importance of the 5' YUNR motif in the target RNA (RNAII) loop L1 of the replication control system of plasmid pIP501. The effect of four individual mutations in L1 was studied in vivo and in vitro. Mutations that maintained the putative U-turn or swapped it from sense to antisense RNA were silent, whereas mutations that eliminated the 5'-YUNR motif showed two- to threefold elevated copy numbers in vivo in correlation with three- to fourfold reduced inhibition rate constants of the complementary RNAIII species in vitro, whereas the half-lives of all RNAIII species were not affected. ENU probing experiments confirmed the U-turn structure for the silent mutation (N-C) and disruption of this structure upon alteration of the invariant U or inversion of the YUNR motif-containing loop. RNA secondary structure probing excluded loop size alterations as a reason for altered inhibition rates. Implications for the pathway and efficiency of RNAII/RNAIII interaction, and hence, pIP501 copy-number control, are discussed.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Heidrich N,Brantl S

doi

10.1016/j.jmb.2003.09.020

keywords:

subject

Has Abstract

pub_date

2003-11-07 00:00:00

pages

917-29

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283603011410

journal_volume

333

pub_type

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