The structure of a highly-conserved picocyanobacterial protein reveals a Tudor domain with an RNA-binding function

J Biol Chem. 2019 Sep 27;294(39):14333-14344. doi: 10.1074/jbc.RA119.007938. Epub 2019 Aug 7.

Abstract

Cyanobacteria of the Prochlorococcus and marine Synechococcus genera are the most abundant photosynthetic microbes in the ocean. Intriguingly, the genomes of these bacteria are strongly divergent even within each genus, both in gene content and at the amino acid level of the encoded proteins. One striking exception to this is a 62-amino-acid protein, termed Prochlorococcus/ Synechococcus hyper-conserved protein (PSHCP). PSHCP is not only found in all sequenced Prochlorococcus and marine Synechococcus genomes, but it is also nearly 100% identical in its amino acid sequence across all sampled genomes. Such universal distribution and sequence conservation suggest an essential cellular role of PSHCP in these bacteria. However, its function is unknown. Here, we used NMR spectroscopy to determine its structure, finding that 53 of the 62 amino acids in PSHCP form a Tudor domain, whereas the remainder of the protein is disordered. NMR titration experiments revealed that PSHCP has only a weak affinity for DNA, but an 18.5-fold higher affinity for tRNA, hinting at an involvement of PSHCP in translation. Isothermal titration calorimetry experiments further revealed that PSHCP also binds single-stranded, double-stranded, and hairpin RNAs. These results provide the first insight into the structure and function of PSHCP, suggesting that PSHCP appears to be an RNA-binding protein that can recognize a broad array of RNA molecules.

Keywords: RNA-binding protein; cyanobacteria; nuclear magnetic resonance (NMR); protein structure; protein–nucleic acid interaction.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Conserved Sequence
  • Intrinsically Disordered Proteins / chemistry*
  • Intrinsically Disordered Proteins / metabolism
  • Prochlorococcus / chemistry
  • Prochlorococcus / metabolism
  • Protein Binding
  • RNA / metabolism
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism
  • Synechococcus / chemistry
  • Synechococcus / metabolism
  • Tudor Domain*

Substances

  • Bacterial Proteins
  • Intrinsically Disordered Proteins
  • RNA-Binding Proteins
  • RNA

Associated data

  • PDB/3PMT
  • PDB/4HCZ
  • PDB/6NNB