Model of a DNA-Protein Complex of the Architectural Monomeric Protein MC1 from Euryarchaea

Françoise Paquet,Bertrand Castaing,Olivier Delalande,Karine Loth,Françoise Culard,Stephane Goffinont,Ulysse Asseline,Celine Landon,Jun-Tao Guo

doi:10.1371/journal.pone.0088809

Abstract

In Archaea the two major modes of DNA packaging are wrapping by histone proteins or bending by architectural non-histone proteins. To supplement our knowledge about the binding mode of the different DNA-bending proteins observed across the three domains of life, we present here the first model of a complex in which the monomeric Methanogen Chromosomal protein 1 (MC1) from Euryarchaea binds to the concave side of a strongly bent DNA. In laboratory growth conditions MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55. Like most proteins that strongly bend DNA, MC1 is known to bind in the minor groove. Interaction areas for MC1 and DNA were mapped by Nuclear Magnetic Resonance (NMR) data. The polarity of protein binding was determined using paramagnetic probes attached to the DNA. The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry. Residues essential to DNA-binding and -bending were highlighted and confirmed by site-directed mutagenesis. It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.

Highlights

The genomic DNA of all organisms across the three domains of life needs to be compacted and functionally organized
To refine our selection these Chemical shift perturbation (CSP) data were compared with the electrostatic potential of Methanogen Chromosomal protein 1 (MC1) and with the flexible regions of MC1 defined by Nuclear Magnetic Resonance (NMR) relaxation data [9]
We assume that residues of MC1, which present CSP after DNAbinding and belong to the basic surface or to the flexible regions, define the DNA-binding surface of MC1 (Figure 1)

Summary

Introduction

The genomic DNA of all organisms across the three domains of life needs to be compacted and functionally organized. Wrappingproteins, bending-proteins and bridging-proteins are involved and it appears that the underlying mechanisms are similar among Bacteria, Archaea and Eukaryota [1]. The two major modes of DNA packaging are 1) wrapping by histone proteins in Eukaryota (H2, H3 and H4 core histones) and Archaea (HMf histones), and 2) bending by architectural non-histone proteins in Bacteria (HU/ IHF/Fis) and Archaea (Cren7/Sul7/MC1). DNA-bridging proteins have been found in Eukaryota (H1linker histone), Archaea (Alba) and Bacteria (H-NS). MC1 is present when Alba is absent. Thermoplasma acidophilum, another Euryarchaea, which is known to lack archaeal histones, encodes the HTa protein, a homolog of bacterial chromatin HU [5,6]

Methods

Results

Conclusion