DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers.
Protein self-organization is essential for the establishment and maintenance of nuclear architecture and for the regulation of gene expression. We have shown previously that the Proline-Rich Homeodomain protein (PRH/Hex) self-assembles to form oligomeric complexes that bind to arrays of PRH binding sites with high affinity and specificity. We have also shown that many PRH target genes contain suitably spaced arrays of PRH sites that allow this protein to bind and regulate transcription. Here, we use analytical ultracentrifugation and electron microscopy to further characterize PRH oligomers. We use the same techniques to show that PRH oligomers bound to long DNA fragments self-associate to form highly ordered assemblies. Electron microscopy and linear dichroism reveal that PRH oligomers can form protein-DNA fibres and that PRH is able to compact DNA in the absence of other proteins. Finally, we show that DNA compaction is not sufficient for the repression of PRH target genes in cells. We conclude that DNA compaction is a consequence of the binding of large PRH oligomers to arrays of binding sites and that PRH is functionally and structurally related to the Lrp/AsnC family of proteins from bacteria and archaea, a group of proteins formerly thought to be without eukaryotic equivalents.
Soufi
Abdenour
A
Institute for Biomedical Research, Birmingham University Medical School, Edgbaston, Birmingham B15 2TT, UK.
Sawasdichai
Anyaporn
A
Shukla
Anshuman
A
Noy
Peter
P
Dafforn
Tim
T
Smith
Corinne
C
Jayaraman
Padma-Sheela
PS
Gaston
Kevin
K
D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D006801:Humans; D020014:K562 Cells; D009690:Nucleic Acid Conformation; D055503:Protein Multimerization; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D014158:Transcription, Genetic
C078492:HHEX protein, human; D018398:Homeodomain Proteins; D014157:Transcription Factors; D004247:DNA