ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes

Abstract

The radiation resistance-repair genes in Deinococcus radiodurans (DR) and E-coli were analyzed in terms of the A, T, C, G nucleotide fluctuations. The studied genes were Rec-A, Rec-Q, and the unique DR PprA gene. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis. Fractal analysis using the Higuchi method gave a fractal dimension increase of the Deinococcus radiodurans genes as compared to E-coli, which is comparable to the enhancement observed in the human HAR1 region (HAR1F gene) over that of the chimpanzee. Near neighbor fluctuation was also studied via the Black-Scholes model where the increment sequence was treated as a random walk series. The Deinococcus radiodurans radiation gene standard deviations were consistently higher than that of the E-coli deviations, and agree with the fractal analysis results. The sequence stacking interaction was studied using the published nucleotide-pair melting free energy values and Deinococcus radiodurans radiation genes were shown to possess larger negative free energies. The high sensitivity of the fractal dimension as a biomarker was tested with correlation analysis of the gamma ray dose versus fractal dimension, and the R square values were found to be above 0.9 (N=5). When compared with other nucleotide sequences such as the rRNA sequences, HAR1 and its chimpanzee counterpart, the higher fluctuation (correlated randomness) and larger negative free energy of a DR radiation gene suggested that a radiation resistance-repair sequence exhibited higher complexity. As the HAR1 nucleotide sequence complexity and its transcription activity of co-expressing cortex protein reelin supported a positive selection event in humans, a similar inference of positive selection of coding genes could be drawn for Deinococcus radiodurans when compared to E-coli. The origin of such a positive selection would be consistent with that of a Martian environment.

Novel methodologies for spectral classification of exon and intron sequences

“…Sixteen 1-sequence numerical representations have been presented and compared to classify untrained exon and intron sequences in the spectral domain, in which the K-Quaternary Code I yields attractive performance. When comparing each of the sixteen windowed 1-sequence numerical representations using WL = [9,15,24] bases to a non-windowed 4-sequence numerical representation (such as the Voss representation), the speed improvement ratio increases as SL increases which favours long nucleotide sequence analysis. The results obtained indicate the methodologies introduced in this article for exon and intron sequence classification are applicable to the genomes of the human and other model organisms.…”

“…The ratio of 4L × log 2 (L) over NW × N × log 2 (N) gives a speed improvement ratio. A plot of the speed improvement ratio against SL for WL = [9,15,24] bases is shown in Figure 10. As seen from Figure 10, it can be observed that a windowed 1-sequence representation with WL = [9,15,24] bases offers a possible speed advantage over a non-windowed 4-sequence representation and the speed improvements increases as SL increases.…”

“…The Single Galois Indicator representation [7,8] maps the CGAT nucleotides to a Galois field of four, GF(4), which is formed by assigning numerical values to the nucleotides as C = 1, G = 3, A = 0, and T = 2 in a nucleotide sequence. This representation suggests that C < G and A < T. In the Paired Nucleotide Atomic Number representation [9], the paired nucleotides are assigned with atomic numbers as A, G = 62 and C, T = 42 respectively. In the Atomic Number representation [9], a numerical sequence is formed by assigning atomic numbers to each nucleotide as C = 58, G = 78, A = 70, and T = 66 in a nucleotide sequence.…”

“…This representation suggests that C < G and A < T. In the Paired Nucleotide Atomic Number representation [9], the paired nucleotides are assigned with atomic numbers as A, G = 62 and C, T = 42 respectively. In the Atomic Number representation [9], a numerical sequence is formed by assigning atomic numbers to each nucleotide as C = 58, G = 78, A = 70, and T = 66 in a nucleotide sequence. The Molecular Mass representation [10] of a nucleotide sequence is formed by mapping the four nucleotides to their molecular masses as C = 110, G = 150, A = 134, and T = 125, respectively.…”

“…In this article, nine 1-sequence numerical representations (Codes 1-9) [5][6][7][8][9][10][11][12][13][14][15][16] are identified though a literature search, which can be grouped under positiveinteger-value, real-value, and complex-value numerical representations. In addition, seven 1-sequence complexvalue numerical representations (Codes 10-16) are derived.…”