Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings

Abstract

We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription factors and the position of peaks in the probability pattern of large thermal openings. Other distinct peaks of the calculated patterns correlate with potential binding sites of DNA-binding proteins. These results suggest that a DNA molecule would more frequently expose the bases that participate in contacts with proteins, which would probably enhance the probability of the latter to reach their targets. It also stands for using this method as a means to analyze DNA sequences based on their intrinsic thermal properties.

Wide-dynamic-range promoters engineered for cyanobacteria

“…Therefore, the increased L21 promoter strength may be due to a more favourable σ subunit binding compared to the L22 promoter. This is supported by similar result when comparing the mutated lac UV5 promoter with the wide-type lac promoter [26]. …”

“…To understand how the thermal opening probability of a pre-melting DNA strand changes after the substitution of bases on indicated positions of a promoter, this was analyzed theoretically with the well-established Peyrard-Bishop-Dauxois (PBD) model via a Monte Carlo method [26]. Due to the sequence-independent stacking term using an averaged constant in this model, 16 L promoters can be only analyzed in four patterns categorized by hydrogen bonds of a modified base pair (Table 1).…”

“… Spontaneous thermal opening probability simulated at 303 K by the average stacking PBD model [26] of a promoter sequence. ( A ) The pattern I (orange dot line) of the R40 promoter is compared to the four patterns, A, B, C and D (cyan line, black line, magenta line, and green line, respectively) simulated from 16 R40 -derived promoters (from L01 to L16).…”

“…A pre-melting promoter DNA with the elevated spontaneous opening probability may be more prone to expose the cognate bases for contacting with a DNA-binding protein such as σ subunit of RNAP and thus to increase the binding probability [26]. The recognition of the -10 element by σ subunit of RNAP has been proposed through the capture of two highly-conserved flipped-out bases and the extensive contact with the sugar-phosphate backbone of each nucleotide in the -10 element on the non-template strand; the recognition is coupled to strand separation and is the key step in initiating transcription [27].…”

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

“…, coherent relatively long-lived transient openings) are a characteristic feature of mammalian core promoters, see for example [37]. Sequences with a relatively high propensity to form bubbles have been found to overlap and affect transcription start sites [35], [38], [39], [40], replication origins [36], [41], correlate with TF binding sites and affect TF binding [42], [43], [44], [45], [46], [47], as well as to play role in formation of non-B-DNA structures [34] and in cytosine methylation [33] …”