When is a transcription factor a NAP?

Abstract

Proteins that regulate transcription often also play an architectural role in the genome. Thus, it has been difficult to define with precision the distinctions between transcription factors and nucleoid-associated proteins (NAPs). Anachronistic descriptions of NAPs as 'histone-like' implied an organizational function in a bacterial chromatin-like complex. Definitions based on protein abundance, regulatory mechanisms, target gene number, or the features of their DNA-binding sites are insufficient as marks of distinction, and trying to distinguish transcription factors and NAPs based on their ranking within regulatory hierarchies or positions in gene-control networks is also unsatisfactory. The terms 'transcription factor' and 'NAP' are ad hoc operational definitions with each protein lying along a spectrum of structural and functional features extending from highly specific actors with few gene targets to those with a pervasive influence on the transcriptome. The Streptomyces BldC protein is used to illustrate these issues.

Figure 1.. BldC contains a MerR-like DNA-binding domain.

Superimposition of the BldC DNA-binding domain (green) [29**] onto that of the MerR-family transcription factor MtaN from B. subtilis (red) [30]. The domains can be overlaid with an rmsd =1.7 Å for 45 corresponding Cα atoms. Note the lack of the dimerization coiled coil in BldC, which is a monomer in solution.

Figure 2.. BldC and Xis bind to DNA by cooperative, head-to-tail oligomerization on direct repeats, producing a continuous nucleoprotein filament of variable length, accompanied by pronounced DNA distortion.

(A) Head-to-tail oligomerization of 4 BldC monomers on the smeA promoter. Each BldC monomer in the nucleoprotein filament forms identical interactions with the next [29**]. (B) Head-to-tail oligomerization of Xis on the 3 direct repeats present in its binding site. Xis monomers bound to the X1, X1.5, and X2 sites are coloured dark salmon, green, and blue, respectively [33]. (C) Structure-based model of an extended BldC–DNA filament. Crystallization of BldC bound to a double-stranded oligonucleotide carrying 2 of the 4 direct repeats found in the BldC binding site from the smeA promoter generated a pseudo-continuous helix in the structure [29**]. Two views are shown. Left is an electrostatic representation showing electropositive and electronegative regions of BldC in blue and red, respectively. Note the continuous protein superstructure also forms a continuous electropositive stripe that tracks along the DNA. Right is a view looking down the axis of the structure. (D) Structure-based model of an extended Xis–DNA filament [33] Copyright (2007) National Academy of Sciences, U.S.A. Units of the Xis–DNA crystal structure were stacked end-to-end to assemble a pseudo-continuous helix with a pitch of ~22 nm. Xis is shown blue and the DNA in orange and red.

Figure 3.. Results of structural homology searches with the BldC structure.

(A) Overlay of the BldC DNA-binding domain (red) with the DNA-binding domain from the sporulation specific B. subtilis RacA protein (green) (rmsd = 2.0 Å for 50 similar Cα atoms) [29**]. (B) Superimposition of the BldC DNA-binding domain (red) with that of the Mycobacteriophage pukovnik Xis protein [60] (rmsd = 1.6 Å for 41 similar Cα atoms). (C) Overlay of DNA-bound BldC (red) [29**] and DNA-bound lambda Xis (yellow) [33], showing that BldC and Xis bind DNA in the same head-to-tail manner.

Figure 4.. Comparison of the DNA-bound structures and modes of DNA binding among MerR-related proteins.

(A) BldC-DNA [29**]. (B) RacA-DNA [32]. (C) TnrA-DNA [34]. (D) MtaN-DNA [30]. The green subunits are shown in the same orientation to highlight the very different dimers and DNA-binding modes for each protein. Note that in the case of the RacA-DNA structure, the RacA dimerization domain has been omitted so the DNA-binding domain can be seen clearly. (E) Summary of the oligomeric states and modes of DNA binding of different MerR-family proteins.