Human Origin Recognition Complex Binds Preferentially to G-quadruplex-preferable RNA and Single-Stranded DNA

J Biol Chem. 2013 Oct 18;288(42):30161-71. doi: 10.1074/jbc.M113.492504. Epub 2013 Sep 3.

Abstract

Origin recognition complex (ORC), consisting of six subunits ORC1-6, is known to bind to replication origins and function in the initiation of DNA replication in eukaryotic cells. In contrast to the fact that Saccharomyces cerevisiae ORC recognizes the replication origin in a sequence-specific manner, metazoan ORC has not exhibited strict sequence-specificity for DNA binding. Here we report that human ORC binds preferentially to G-quadruplex (G4)-preferable G-rich RNA or single-stranded DNA (ssDNA). We mapped the G-rich RNA-binding domain in the ORC1 subunit, in a region adjacent to its ATPase domain. This domain itself has an ability to preferentially recognize G4-preferable sequences of ssDNA. Furthermore, we found, by structure modeling, that the G-rich RNA-binding domain is similar to the N-terminal portion of AdoMet_MTase domain of mammalian DNA methyltransferase 1. Therefore, in contrast with the binding to double-stranded DNA, human ORC has an apparent sequence preference with respect to its RNA/ssDNA binding. Interestingly, this specificity coincides with the common signature present in most of the human replication origins. We expect that our findings provide new insights into the regulations of function and chromatin binding of metazoan ORCs.

Keywords: DNA Methyltransferase; DNA Replication; DNA-binding Protein; G-quadruplex; ORC; Protein Structure; RNA-binding Protein; Replication Origin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA Modification Methylases / chemistry
  • DNA Modification Methylases / genetics
  • DNA Modification Methylases / metabolism
  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Humans
  • Multiprotein Complexes / chemistry*
  • Multiprotein Complexes / genetics
  • Multiprotein Complexes / metabolism
  • Nucleic Acid Heteroduplexes / chemistry*
  • Nucleic Acid Heteroduplexes / genetics
  • Nucleic Acid Heteroduplexes / metabolism
  • Origin Recognition Complex / chemistry*
  • Origin Recognition Complex / genetics
  • Origin Recognition Complex / metabolism
  • Protein Structure, Tertiary
  • RNA / chemistry*
  • RNA / genetics
  • RNA / metabolism
  • Saccharomyces cerevisiae
  • Xenopus laevis

Substances

  • DNA, Single-Stranded
  • Multiprotein Complexes
  • Nucleic Acid Heteroduplexes
  • Origin Recognition Complex
  • RNA
  • DNA Modification Methylases