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Proceedings Paper

Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology
Author(s): Todd Holden; G. Tremberger; E. Cheung; R. Subramaniam; R. Sullivan; P. Schneider; A. Flamholz; P. Marchese; O. Hiciano; H. Yao; D. Lieberman; T. Cheung
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Paper Abstract

Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface, could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could exist in extremely cold conditions (such as that which existed on early Mars) where demands on gene activity are low. In addition, the comparative study of the Methanococcoides burtonii cold shock domain sequence has provided further support for the correlation between multitasking capacity and fractal dimension.

Paper Details

Date Published: 28 August 2008
PDF: 11 pages
Proc. SPIE 7097, Instruments, Methods, and Missions for Astrobiology XI, 70970V (28 August 2008); doi: 10.1117/12.794398
Show Author Affiliations
Todd Holden, CUNY Queensborough Community College (United States)
G. Tremberger, CUNY Queensborough Community College (United States)
E. Cheung, CUNY Queensborough Community College (United States)
R. Subramaniam, CUNY Queensborough Community College (United States)
R. Sullivan, CUNY Queensborough Community College (United States)
P. Schneider, CUNY Queensborough Community College (United States)
A. Flamholz, CUNY Queensborough Community College (United States)
P. Marchese, CUNY Queensborough Community College (United States)
O. Hiciano, CUNY Queensborough Community College (United States)
H. Yao, CUNY Queensborough Community College (United States)
D. Lieberman, CUNY Queensborough Community College (United States)
T. Cheung, CUNY Queensborough Community College (United States)


Published in SPIE Proceedings Vol. 7097:
Instruments, Methods, and Missions for Astrobiology XI
Richard B. Hoover; Gilbert Victor Levin; Alexei Yu. Rozanov; Paul C.W. Davies, Editor(s)

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