DNA Curvature In Silico Analysis of Arthropod Genes Promoter
Gouveia F. de S.1, Fiorini, A. 2, and Fernandez, M.A1.
1Depto. de Biologia Celular e Genética, DBC, Universidade Estadual de Maringá, UEM, Paraná., Brasil, e-mail: mafernandez@uem.br
2Centro Universitário de Maringá, CESUMAR, Paraná, Brasil.
TATA-box regions from gene promoters present short sequence base repeats that permit flexibility in this segment. It is described that intrinsic DNA curvature in the TATA-box is a prerequisite for the TPB binding. The presence of dA/dT tracts of 2 at 6 nucleotides, phased with the helical turn, induces a sequence-directed curvature. Although the functional role of this structure remains unclear, it is discussed if the intrinsic curvature could be necessary for transcription regulation. Our laboratory develops analysis in the Rhynchosciara americana C3-22 amplified gene promoter region, in which were identified intrinsic DNA bent sites through electrophoresis differential analysis. Comparative analyses between the different organisms TATA-box regions may allow the verification of the structure that forms this region. In this work, the helical parameters and 2D modeling of the 625 bp sequence containing the secretion protein genes TATA box region of RaC3 from Rhynchosciara americana, Sgs 3 from Drosophila melanogaster, AaHI from Androctonus australis, BhC4-1 and BhB-10 from Bradygia hygida, TpC4B from Thrichosia pubescens and the fib-H gene from Bombyx mori are described. These segments were analyzed by Map15a and 3D15m1 software for mapping and 2D modeling analysis, respectively. The parameter ENDS ratio (ratio of the contour length of the segment’s helical axis to the shortest distance between the fragments ends) was used to calculate peaks of curvature, with 120 bp window width and 10 bp step. The results showed that all ENDS ratio peaks values were higher than 1.12 and co-localized with the TATA-box segment, what is confirmed by the 2D modeling analysis. The structural figures can be grouped in three clusters, one with a curvature composed by the main ENDS ratio sharp peak and no bending flanking sequences, composed by the promoter segments from TpC4B and AaH1; a second group composed by BhC4-1, RaC3 and fib-H that showed a sharp peak and bending flanking sequences that cooperate with the curvature in the TATA-box region, and a third group composed by the Sgs-3 and the BhB-10, that has no sharp peak but with bending flanking sequences. These structural similarities indicate that sequence-directed curvature could be a conserved characteristic of arthropod’s TATA-box regions of protein secretion genes, irrespectively of the secretion type.
Supported by: CAPES, CNPq, TWAS, FINEP, Fundação Araucária and Complexo de Centrais de Apoio a Pesquisa, COMCAP-UEM.
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