Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Todd Holden; G. Tremberger Jr.; E. Cheung; R. Subramaniam; N. Gadura; P. Schneider; R. Sullivan; A. Flamholz; D. Lieberman; T. D. Cheung

doi:10.1117/12.825827

11 September 2009 Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Todd Holden, G. Tremberger Jr., E. Cheung, R. Subramaniam, N. Gadura, P. Schneider, R. Sullivan, A. Flamholz, D. Lieberman, T. D. Cheung

Author Affiliations +

Proceedings Volume 7441, Instruments and Methods for Astrobiology and Planetary Missions XII; 74410R (2009) https://doi.org/10.1117/12.825827
Event: SPIE Optical Engineering + Applications, 2009, San Diego, California, United States

Abstract

The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. 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 in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R²~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R² slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R² ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

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Todd Holden, G. Tremberger Jr., E. Cheung, R. Subramaniam, N. Gadura, P. Schneider, R. Sullivan, A. Flamholz, D. Lieberman, and T. D. Cheung "Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes", Proc. SPIE 7441, Instruments and Methods for Astrobiology and Planetary Missions XII, 74410R (11 September 2009); https://doi.org/10.1117/12.825827

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KEYWORDS

Fractal analysis

Image information entropy

Proteins

Mars

Bacteria

Silver

Resistance

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