Integration host factor of Mycobacterium tuberculosis, mIHF, compacts DNA by a bending mechanism

PLoS One. 2013 Jul 26;8(7):e69985. doi: 10.1371/journal.pone.0069985. Print 2013.

Abstract

The bacterial chromosomal DNA is folded into a compact structure called as 'nucleoid' so that the bacterial genome can be accommodated inside the cell. The shape and size of the nucleoid are determined by several factors including DNA supercoiling, macromolecular crowding and nucleoid associated proteins (NAPs). NAPs bind to different sites of the genome in sequence specific or non-sequence specific manner and play an important role in DNA compaction as well as regulation. Until recently, few NAPs have been discovered in mycobacteria owing to poor sequence similarities with other histone-like proteins of eubacteria. Several putative NAPs have now been identified in Mycobacteria on the basis of enriched basic residues or histone-like "PAKK" motifs. Here, we investigate mycobacterial Integration Host Factor (mIHF) for its architectural roles as a NAP using atomic force microscopy and DNA compaction experiments. We demonstrate that mIHF binds DNA in a non-sequence specific manner and compacts it by a DNA bending mechanism. AFM experiments also indicate a dual architectural role for mIHF in DNA compaction as well as relaxation. These results suggest a convergent evolution in the mechanism of E. coli and mycobacterial IHF in DNA compaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Cloning, Molecular
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism*
  • Genome, Bacterial
  • Integration Host Factors / genetics
  • Integration Host Factors / metabolism*
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / metabolism*
  • Open Reading Frames
  • Protein Binding
  • Tuberculosis / microbiology*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Integration Host Factors

Grants and funding

AM, AB and MV thank Council of Scientific and Industrial Research, India (CSIR); DK acknowledges Department of Science and Technology-Inspire (DST-Inspire); and AKM acknowledges Department of Biotechnology - BioInformatics National Certification (DBT-BINC) India for research fellowships. VT acknowledges fellowship from Innovative Young Biotechnology Award, DBT, India. This work was supported by GAP-0060 project grant of DST, India to BT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.