Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues.
HMGB proteins are abundant non-histone components of eukaryotic chromatin. The biological function of DNA sequence-nonspecific HMGB proteins is obscure. These proteins are composed of one or two conserved HMG box domains, each forming three alpha-helices that fold into a sequence-nonspecific DNA-binding module recognizing the DNA minor groove. Box A and box B homology domains have subtle sequence differences such that box B domains bend DNA strongly while DNA bending by isolated box A domains is weaker. Both box A and box B domains preferentially bind to distorted DNA structures. Here we show using DNA cyclization kinetics assays in vitro and Escherichia coli DNA looping assays in vivo that an isolated HMG box A domain derived from human HMGB2 folds poorly and does not enhance apparent DNA flexibility. Surprisingly, substitution of a small number of cationic residues from the N-terminal leader of a functional yeast box B protein, Nhp6Ap, confers the ability to enhance DNA flexibility. These results demonstrate important roles for cationic leader amino acids in HMGB folding, DNA interaction, and DNA bending.
Sebastian
Nadia T
NT
Department of Chemistry, Creighton University, 2500 California Place, Omaha, Nebraska 68178, USA.
Bystry
Emily M
EM
Becker
Nicole A
NA
Maher
L James
LJ
D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics; D005454:Fluorescence Polarization; D024742:HMG-Box Domains / Q000502:physiology*; D024002:HMGB Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D024261:HMGB2 Protein / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D024001:HMGN Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007763:Lac Operon / Q000235:genetics; D009690:Nucleic Acid Conformation; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding / Q000235:genetics; D021382:Protein Sorting Signals / Q000235:genetics; D017433:Protein Structure, Secondary; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D024002:HMGB Proteins; D024261:HMGB2 Protein; D024001:HMGN Proteins; C086471:NHP6A protein, S cerevisiae; D010446:Peptide Fragments; D021382:Protein Sorting Signals; D011993:Recombinant Fusion Proteins; D029701:Saccharomyces cerevisiae Proteins; C116822:hns protein, E coli; D004247:DNA