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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Functional equivalence of an evolutionarily conserved RNA binding module.

Melissa L Wells1, Stephanie N Hicks1, Lalith Perera2

  • 1From the Signal Transduction Laboratory and.

The Journal of Biological Chemistry
|August 21, 2015
PubMed
Summary

The tandem zinc finger (TZF) domain of tristetraprolin (TTP) proteins is functionally interchangeable across evolutionarily distant species. This conserved RNA-binding domain from yeast, insects, plants, and humans can substitute for the native TZF domain in fission yeast, maintaining mRNA regulation.

Keywords:
RNA binding proteinRNA turnovermRNA decayyeast geneticszinc finger

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Tristetraprolin (TTP) proteins regulate mRNA turnover by binding to AU-rich elements.
  • The conserved tandem zinc finger (TZF) domain is the primary RNA-binding region in TTP family proteins.
  • Sequence variation in TZF domains raises questions about functional specificity in RNA binding and decay.

Purpose of the Study:

  • To investigate the functional interchangeability of TZF domains from evolutionarily distant species.
  • To determine if TZF domains from humans, silkworms, yeast, and plants can replace the native TZF domain in fission yeast.

Main Methods:

  • Utilized knockin techniques in Schizosaccharomyces pombe to replace the native Zfs1 TZF domain.
  • Introduced TZF domains from human TTP, Bombyx mori, Candida guilliermondii, and Chromolaena odorata.
  • Assessed functional complementation by measuring target transcript levels and flocculation phenotypes.
  • Characterized RNA binding affinity of recombinant TZF peptides using AU-rich RNA oligonucleotides.

Main Results:

  • TZF domains from human, silkworm, yeast, and plant origins fully substituted for the native S. pombe Zfs1 TZF domain.
  • Functional complementation was confirmed by restoration of normal transcript levels and phenotypes.
  • Recombinant TZF peptides demonstrated comparable high-affinity binding to AU-rich RNA.

Conclusions:

  • The TZF domains of TTP family proteins are functionally interchangeable across a wide evolutionary range.
  • This interchangeability extends to both mRNA binding and decay promotion functions.
  • The conserved structure of the TZF domain underlies its conserved function in post-transcriptional gene regulation.