Abstract
MC1, a monomeric nucleoid-associated protein (NAP), is structurally unrelated to other DNA-binding proteins. The protein participates in the genome organization of several Euryarchaea species through an atypical compaction mechanism. It is also involved in DNA transcription and cellular division through unknown mechanisms. We determined the 3D solution structure of a new DNA-protein complex formed by MC1 and a strongly distorted 15 base pairs DNA. While the protein just needs to adapt its conformation slightly, the DNA undergoes a dramatic curvature (the first two bend angles of 55° and 70°, respectively) and an impressive torsional stress (dihedral angle of 106°) due to several kinks upon binding of MC1 to its concave side. Thus, it adopts a V-turn structure. For longer DNAs, MC1 stabilizes multiple V-turn conformations in a flexible and dynamic manner. The existence of such V-turn conformations of the MC1-DNA complexes leads us to propose two binding modes of the protein, as a bender (primary binding mode) and as a wrapper (secondary binding mode). Moreover, it opens up new opportunities for studying and understanding the repair, replication and transcription molecular machineries of Archaea.
Highlights
In the three domains of life, DNA-binding proteins are involved in genome organization, packaging it into eukaryotic organelles or into the cell, while efficiently accommodating DNA-based processes such as transcription, replication and repair
Twelve other NOEs were unambiguously identified to the side chain protons of Trp[74] (HB1, HB2, HD1, HE3 and HZ2) in contact with H2 and sugar protons of A15 (H1′) and T16 (H2′, H3′, H5′) and amino protons H21/22 of G17, all located in the minor groove
The dynamic nature of the free DNA15bp structure enables Methanogen Chromosomal protein 1 (MC1) to transiently select narrow minor groove segments (A-tract), which can be further stabilized through Coulombic interactions with the electropositive binding surface of the protein (Arg[4], Lys[54], His[56], Lys[86], Lys91)
Summary
In the three domains of life, DNA-binding proteins are involved in genome organization, packaging it into eukaryotic organelles or into the cell (in bacteria or archaea), while efficiently accommodating DNA-based processes such as transcription, replication and repair. In Crenarchaea lacking histone proteins, Cren[7] is always present whereas Sul[7] ( known as Sso7d or Sac7d) is restricted to Sulfolobus[8,9] They non- bind to DNA by inserting www.nature.com/scientificreports/. The dimeric HU-family proteins present a compact core of α-helices with two emerging flexible β-ribbon arms[14] They form low-affinity HU-DNA complexes without sequence specificity and high-affinity complexes with flexible or bent DNA, such as single-strand nicks and gaps, and bulged and branched DNA structures[15,16,17]. It was proposed to be involved in DNA transcription (in vitro essays)[22] and cellular division (proteomics by LCMS)[23,24], through as yet unknown mechanisms This small basic monomeric protein of 93 residues (UniProt P12770) is structurally unrelated to other DNA-binding proteins[25,26]. When DNA is bound to MC1, it is protected against thermal denaturation[18] and radiolysis[28]
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