Shot-gun proteomic analysis of mitochondrial D-loop DNA binding proteins: Identification of mitochondrial histones

Yon Sik Choi, Jae Hoon Jeong, Hye Ki Min, Hee Jung Jung, Daehee Hwang, Sang Won Lee, Youngmi Kim Pak

Research output: Contribution to journalArticlepeer-review

56 Citations (Scopus)


Transcription and replication of mitochondrial DNA (mtDNA) are regulated by nuclear DNA-encoded proteins that are targeted into mitochondria. A decrease in mtDNA copy number results in mitochondrial dysfunction, which may lead to insulin resistance and metabolic syndromes. We analyzed mitochondrial proteins that physically bind to human mitochondrial D-loop DNA using a shot-gun proteomics approach following protein enrichment by D-loop DNA-linked affinity chromatography. A total of 152 D-loop DNA binding proteins were identified by peptide sequencing using ultra high pressure capillary reverse-phase liquid chromatography/tandem mass spectrometry. Bioinformatic analysis showed that 68 were mitochondrial proteins, 96 were DNA/RNA/protein binding proteins and 114 proteins might form a complex via protein-protein interactions. Histone family members of H1, H2A, H2B, H3, and H4, were detected in abundance among them. In particular, histones H2A and H2B were present in the mitochondrial membrane as integral membrane proteins and not bound directly to mtDNA inside the organelle. Histones H1.2, H3 and H4 were associated with the outer mitochondrial membrane. Silencing of H2AX expression inhibited mitochondrial protein transport. Our data suggests that many mitochondrial proteins may reside in multiple subcellular compartments like H2AX and exert multiple functions.

Original languageEnglish
Pages (from-to)1523-1536
Number of pages14
JournalMolecular BioSystems
Issue number5
Publication statusPublished - 2011 May 1

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology


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