ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes

Todd Holden; R. Subramaniam; R. Sullivan; E. Cheung; C. Schneider; G. Tremberger Jr.; A. Flamholz; D. H. Lieberman; T. D. Cheung

doi:10.1117/12.732283

1 October 2007 ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes

Todd Holden, R. Subramaniam, R. Sullivan, E. Cheung, C. Schneider, G. Tremberger Jr., A. Flamholz, D. H. Lieberman, T. D. Cheung

Author Affiliations +

Proceedings Volume 6694, Instruments, Methods, and Missions for Astrobiology X; 669417 (2007) https://doi.org/10.1117/12.732283
Event: Optical Engineering + Applications, 2007, San Diego, California, United States

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.

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Todd Holden, R. Subramaniam, R. Sullivan, E. Cheung, C. Schneider, G. Tremberger Jr., A. Flamholz, D. H. Lieberman, and T. D. Cheung "ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes", Proc. SPIE 6694, Instruments, Methods, and Missions for Astrobiology X, 669417 (1 October 2007); https://doi.org/10.1117/12.732283

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