RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression

Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5651-6. doi: 10.1073/pnas.1200318109. Epub 2012 Mar 26.

Abstract

The half-a-tetratricopeptide repeat (HAT) motif is a helical repeat motif found in proteins that influence various aspects of RNA metabolism, including rRNA biogenesis, RNA splicing, and polyadenylation. This functional association with RNA suggested that HAT repeat tracts might bind RNA. However, RNA binding activity has not been reported for any HAT repeat tract, and recent literature has emphasized a protein binding role. In this study, we show that a chloroplast-localized HAT protein, HCF107, is a sequence-specific RNA binding protein. HCF107 consists of 11 tandem HAT repeats and short flanking regions that are also predicted to form helical hairpins. The minimal HCF107 binding site spans ∼11 nt, consistent with the possibility that HAT repeats bind RNA through a modular one repeat-1 nt mechanism. Binding of HCF107 to its native RNA ligand in the psbH 5' UTR remodels local RNA structure and protects the adjacent RNA from exonucleases in vitro. These activities can account for the RNA stabilizing, RNA processing, and translational activation functions attributed to HCF107 based on genetic data. We suggest that analogous activities contribute to the functions of HAT domains found in ribonucleoprotein complexes in the nuclear-cytosolic compartment.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 5' Untranslated Regions / genetics
  • Amino Acid Sequence
  • Arabidopsis / enzymology
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / chemistry
  • Arabidopsis Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Electrophoretic Mobility Shift Assay
  • Exoribonucleases / metabolism
  • Gene Expression Regulation, Plant*
  • Membrane Proteins / chemistry
  • Membrane Proteins / metabolism*
  • Molecular Sequence Data
  • Mutant Proteins / chemistry
  • Mutant Proteins / metabolism
  • Nucleic Acid Conformation
  • Plant Proteins / chemistry
  • Plant Proteins / metabolism*
  • Protein Binding
  • Protein Biosynthesis
  • RNA, Plant / genetics*
  • RNA, Plant / metabolism
  • Repetitive Sequences, Amino Acid
  • Zea mays / enzymology
  • Zea mays / genetics*

Substances

  • 5' Untranslated Regions
  • Arabidopsis Proteins
  • HCF107 protein, Arabidopsis
  • Membrane Proteins
  • Mutant Proteins
  • Plant Proteins
  • RNA, Plant
  • Exoribonucleases
  • 5'-exoribonuclease