A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18554-9. doi: 10.1073/pnas.1407634112. Epub 2014 Dec 15.

Abstract

Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. Here we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an "L"-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conserved basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Thus, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.

Keywords: Puf-A; Puf6; crystal structure; mRNA localization; ribosome biogenesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Crystallography, X-Ray
  • Humans
  • Protein Binding
  • Protein Folding
  • Protein Structure, Tertiary
  • RNA Precursors / chemistry*
  • RNA Precursors / genetics
  • RNA Precursors / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Fungal / chemistry*
  • RNA, Fungal / genetics
  • RNA, Fungal / metabolism
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Saccharomyces cerevisiae / chemistry*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism

Substances

  • PUM1 protein, human
  • Puf6 protein, S cerevisiae
  • RNA Precursors
  • RNA, Fungal
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins

Associated data

  • PDB/4WZR
  • PDB/4WZW