Toward a Universal Structural and Energetic Model for Prokaryotic Promoters

Abstract

With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ∼16,500 promoters of 12 prokaryotes representing two kingdoms in their structure and energetics. Twenty-eight fundamental parameters of DNA structure including backbone angles, basepair axis, and interbasepair and intrabasepair parameters were used, and information was extracted from x-ray crystallography data. Three parameters (solvation energy, hydrogen-bond energy, and stacking energy) were selected for creating energetics profiles using in-house programs. DNA of promoter regions was found to be inherently designed to undergo a change in every parameter undertaken for the study, in all prokaryotes. The change starts from some distance upstream of TSSs and continues past some distance from TSS, hence giving a signature state to promoter regions. These signature states might be the universal hidden codes recognized by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three-dimensional structures quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. -11, -35, and -75 positions relative to TSS) of promoters reveal novel to our knowledge and pointed insights for RNAP interaction at these locations; it could be correlated with how some particular structural changes at the -11 region may allow insertion of RNAP amino acids in interbasepair space as well as facilitate the flipping out of bases from the DNA duplex.

Intron exon boundary junctions in human genome have in-built unique structural and energetic signals

“…The structural parameters include—nine backbone (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Chi, Phase and Amplitude), eight inter-BP (Shift, Slide, Rise, Tilt, Roll, Twist, H-Rise and H-Twist), six intra-BP (Shear, Stretch, Stagger, Buckle, Propel and Opening) and five BP-axis (X Displacement, Y Displacement, Inclination, Tip and Axis-Bend) parameters. The values of these parameters were calculated by applying Curves+ webserver ( 44 ) on 74 B-DNA crystal structures obtained from NDB database ( Supplementary Table S1 .1) ( 55 ). After calculating values for all the parameters for each B-DNA structure, all occurrences of unique 10 di-nucleotide steps in the 5′ to 3′ direction were considered for each parameter and the average of all the occurrences were calculated.…”

“…These boundary sequences were subjected to structural and energetic characterization using 28 structural and three energy parameters. To obtain numeric values of conformational parameters for the unique di-nucleotides steps, we downloaded the crystals structures of B-DNA from Nucleic Acids Database (NDB) ( 55 ) and applied the Curves+ webserver ( 31 ) on these structures for the same. In-house programs were used for calculating the energy parameters ( 53 ).…”

Molecular dynamics simulation-based trinucleotide and tetranucleotide level structural and energy characterization of the functional units of genomic DNA

“…Our Lab has been investigating the energetics of DNA for the past 20 years, and we have demonstrated the importance of solvation, stacking, and hydrogen bond energy in identifying the distinct genomic functional units. [30][31][32][33][34]52,68,69 Apart from the energy parameters, in recent years, we have explored the complete structural profile of DNA in and around various important motifs by taking into consideration the individual parameters belonging to four major DNA structural categories. 6,17,30 For each energy and structural parameter, individual TSS and CDS sequences from respective organisms were converted to their numerical profiles; these were then averaged at each position and were used for plotting (Fig.…”

“…[30][31][32][33][34]52,68,69 Apart from the energy parameters, in recent years, we have explored the complete structural profile of DNA in and around various important motifs by taking into consideration the individual parameters belonging to four major DNA structural categories. 6,17,30 For each energy and structural parameter, individual TSS and CDS sequences from respective organisms were converted to their numerical profiles; these were then averaged at each position and were used for plotting (Fig. 2 and 3).…”

“…Since there exists no universal model for the identification and characterization of these genomic elements, it is necessary to come up with a chemistry-based approach to annotation. In our previous research communications, 6,17,[30][31][32][33][34] we have elucidated the importance of the structural and energy-based profiling of the DNA elements. Likewise, other groups have also focused on capturing the structural and energy signals of various regions by considering properties like free energy, A-philicity, curvature, bendability, inter-BP properties, and DNA duplex stability under stress.…”