DNA topology confers sequence specificity to nonspecific architectural proteins

Abstract

Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover, the placement of HU along loops with the "wild-type" spacing found in the Escherichia coli lactose (lac) and galactose (gal ) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex. Thus, an architectural protein with no discernible DNA sequencerecognizing features becomes site-specific and potentially assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations. The protein responds to DNA shape and deformability-the stiff, naturally straight double-helical structure-rather than to the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context of chromatin, may influence repressoroperator interactions in the context of the bacterial nucleoid.NA behaves differently in a cellular milieu than in aqueous salt solution. Proteins attach to widely spaced sites along genomic sequences in vivo and force the intervening DNA into loops much shorter in length than those expected from the natural deformational properties of the double helix. For example, the control of gene expression in Escherichia coli entails the formation of short DNA loops, some ∼100 bp steps in length, that preclude access of RNA polymerase to the signals needed to transcribe the enzymes encoded within various operons (1, 2). DNA of the same length tends to be highly extended in vitro, with very low chances of closing spontaneously into a loop (3, 4).Aside from the proteins that hold specific sequences at the ends of short DNA loops in place, the cellular environment includes a number of other components that influence the properties of DNA loops. For example, the naturally abundant, nonspecific E. coli heat-unstable (HU) protein plays important roles both in cellular processing and in shaping the architecture of the bacterial nucleoid. The dimeric protein introduces large deformations in DNA-sharp bends, helical untwisting, and helical axis dislocation (5)-that are central to its activity. The binding of HU to an AT-rich sequence element stabilizes loops important for repression of the galactose (ga...

Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation

“…This phenomenon of cooperative kink formation due to bending in small DNA loops has also been seen experimentally with cryo-EM (31), although the sequence dependence of this phenomenon could not be determined. Simulation studies of the DNA loop stabilizing protein HU have demonstrated a cooperative uptake of proteins that introduce sharp kinks in DNA at antipodal sites along a closed DNA circle, highlighting the critical role played by DNA topology in inducing site-specific recognition by otherwise non-specific DNA binding proteins (43). …”

A stochastic reaction-diffusion model for protein aggregation on DNA

“…28 Their numerical simulations revealed a number of interesting physical mechanisms, including HU-assisted loop formation 24,26 and DNA-directed sequence speci¯city of nonspeci¯c bending proteins. 25 However, all the above mentioned models did not reveal the mechanism underlying the HU cooperative clustering and the related topological patterns.…”

“…Olson and co-workers took the modeling of HU-DNA complexes beyond the traditional statistical mechanics approach by considering realistic three-dimensional (3D) structural and mechanical features. [19][20][21][22][23][24][25][26][27] The fact that their coarse-grained model was based on elastic forces made the realization of a great number of atoms possible. 28 Their numerical simulations revealed a number of interesting physical mechanisms, including HU-assisted loop formation 24,26 and DNA-directed sequence speci¯city of nonspeci¯c bending proteins.…”

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

“…The formation of the GalR loop requires both negatively supercoiled DNA and HU (Lia et al 2003). Simulations of the binding of HU to the GalR and LacR loops indicate that DNA superhelicity can direct the binding of HU to a specific site within the loop and confer an optimal trajectory on the looped DNA for loop closure by the repressor protein (Wei et al 2014). By untwisting constrained DNA, HU has the potential to alter the average helical repeat in the loop and so enable optimal interactions.…”