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Mapping interactions between the rna chaperone fino and its rna targets

Academic Article
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Overview

authors

  • Arthur, D. C.
  • Edwards, R. A.
  • Tsutakawa, S.
  • Tainer, John
  • Frost, L. S.
  • Glover, J. N. M.

publication date

  • May 2011

journal

  • Nucleic Acids Research  Journal

abstract

  • Bacterial conjugation is regulated by two-component repression comprising the antisense RNA FinP, and its protein co-factor FinO. FinO mediates base-pairing of FinP to the 5'-untranslated region (UTR) of traJ mRNA, which leads to translational inhibition of the transcriptional activator TraJ and subsequent down regulation of conjugation genes. Yet, little is known about how FinO binds to its RNA targets or how this interaction facilitates FinP and traJ mRNA pairing. Here, we use solution methods to determine how FinO binds specifically to its minimal high affinity target, FinP stem-loop II (SLII), and its complement SLIIc from traJ mRNA. Ribonuclease footprinting reveals that FinO contacts the base of the stem and the 3' single-stranded tails of these RNAs. The phosphorylation or oxidation of the 3'-nucleotide blocks FinO binding, suggesting FinO binds the 3'-hydroxyl of its RNA targets. The collective results allow the generation of an energy-minimized model of the FinO-SLII complex, consistent with small-angle X-ray scattering data. The repression complex model was constrained using previously reported cross-linking data and newly developed footprinting results. Together, these data lead us to propose a model of how FinO mediates FinP/traJ mRNA pairing to down regulate bacterial conjugation.

subject areas

  • 5' Untranslated Regions
  • Bacterial Outer Membrane Proteins
  • Bacterial Proteins
  • Binding Sites
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA, Antisense
  • RNA, Bacterial
  • RNA, Messenger
  • RNA-Binding Proteins
  • Ribonuclease, Pancreatic
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Identity

PubMed Central ID

  • PMC3105414

International Standard Serial Number (ISSN)

  • 0305-1048

Digital Object Identifier (DOI)

  • 10.1093/nar/gkr025

PubMed ID

  • 21278162
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Additional Document Info

start page

  • 4450

end page

  • 4463

volume

  • 39

issue

  • 10

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