Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner.
Architectural DNA proteins play important roles in the chromosomal DNA organization and global gene regulation in living cells. However, physiological functions of some DNA-binding proteins from archaea remain unclear. Recently, several abundant DNA-architectural proteins including histones, Alba, and TrmBL2 have been identified in model euryarchaeon Thermococcus kodakarensis. Although histones and Alba proteins have been previously characterized, the DNA binding properties of TrmBL2 and its interplay with the other major architectural proteins in the chromosomal DNA organization and gene transcription regulation remain largely unexplored. Here, we report single-DNA studies showing that at low ionic strength (<300 mM KCl), TrmBL2 binds to DNA largely in non-sequence-specific manner with positive cooperativity, resulting in formation of stiff nucleoprotein filamentous patches, whereas at high ionic strength (>300 mM KCl) TrmBL2 switches to more sequence-specific interaction, suggesting the presence of high affinity TrmBL2-filament nucleation sites. Furthermore, in vitro assays indicate the existence of DNA binding competition between TrmBL2 and archaeal histones B from T. kodakarensis, which can be strongly modulated by DNA supercoiling and ionic strength of surrounding solution. Overall, these results advance our understanding of TrmBL2 DNA binding properties and provide important insights into potential functions of architectural proteins in nucleoid organization and gene regulation in T. kodakarensis.
Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore.
Artem K
AK
Efremov
Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; School of Physics, Shandong University, Jinan 250100, China.
Yuanyuan
Y
Qu
Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan.
Hugo
H
Maruyama
Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 119077.
Ci J
CJ
Lim
Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan. Electronic address: takeyasu@lif.kyoto-u.ac.jp.
Kunio
K
Takeyasu
Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 119077. Electronic address: phyyj@nus.edu.sg.
Jie
J
Yan
D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D019847:Chromosomes, Archaeal / Q000235:genetics / Q000378:metabolism*; D019641:DNA, Archaeal / Q000235:genetics / Q000378:metabolism*; D004278:DNA, Superhelical / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D019712:Thermococcus / Q000235:genetics / Q000378:metabolism*
D019843:Archaeal Proteins; D019641:DNA, Archaeal; D004278:DNA, Superhelical; D006657:Histones; D012097:Repressor Proteins
DNA supercoiling; DNA-binding protein; archaea; atomic force microscopy (AFM); extreme thermophile; gene regulation; magnetic tweezers; protein-DNA interaction; single-molecule biophysics