In mesophilic prokaryotes, the DNA-binding protein HU participates in nucleoid 
organization as well as in regulation of DNA-dependent processes. Little is 
known about nucleoid organization in thermophilic eubacteria. We show here that 
HU from the hyperthermophilic eubacterium Thermotoga maritima HU bends DNA and 
constrains negative DNA supercoils in the presence of topoisomerase I. However, 
while binding to a single site occludes approximately 35 bp, association of T. 
maritima HU with DNA of sufficient length to accommodate multiple protomers 
results in an apparent shorter occluded site size. Such complexes consist of 
ordered arrays of protomers, as revealed by the periodicity of DNase I cleavage. 
Association of TmHU with plasmid DNA yields a complex that is remarkably 
resistant to DNase I-mediated degradation. TmHU is the only member of this 
protein family capable of occluding a 35 bp nonspecific site in duplex DNA; we 
propose that this property allows TmHU to form exceedingly stable associations 
in which DNA flanking the kinks is sandwiched between adjacent proteins. We 
suggest that T. maritima HU serves an architectural function when associating 
with a single 35 bp site, but generates a very stable and compact aggregate at 
higher protein concentrations that organizes and protects the genomic DNA.