Phaeodactylum tricornutum photosynthesis and Thalassiosira pseudonana bio-silica formation genes nucleotide fluctuations

Todd Holden; P. Marchese; G. Tremberger Jr.; E. Cheung; R. Subramaniam; R. Sullivan; P. Schneider; A. Flamholz; M. Huerta; D. Lieberman; T. Cheung

doi:10.1117/12.794414

28 August 2008 Phaeodactylum tricornutum photosynthesis and Thalassiosira pseudonana bio-silica formation genes nucleotide fluctuations

Todd Holden, P. Marchese, G. Tremberger Jr., E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, M. Huerta, D. Lieberman, T. Cheung

Author Affiliations +

Proceedings Volume 7097, Instruments, Methods, and Missions for Astrobiology XI; 70970R (2008) https://doi.org/10.1117/12.794414
Event: Optical Engineering + Applications, 2008, San Diego, California, United States

Abstract

Diatom bioactivity has been reported to be responsible for about 20% of carbon fixation globally and together with other photosynthetic organisms, the bioactivity can be monitored via satellite ocean imaging. The bioinformatics embedded in the nucleotide fluctuations of photosynthesis and bio-silicate genes in diatoms were studied. The recently reported phosphoenolpyruvate carboxylase PEPC1 and PEPC2 C4-like photosynthesis genes in Phaeodactylum tricornutum were found to have similar fractal dimensions of about 2.01. In comparison, the green alga Chlamydomonas reinhardtii PEPC1 and PEPC2 genes have fractal dimensions of about 2.05. The PEPC CpG dinucleotide content is 8% in P. tricornutum and 10% in C. reinhardtii. Further comparison of the cell wall protein gene showed that the VSP1 gene sequence in C. reinhardtii has a fractal dimension of 2.03 and the bio-silica formation silaffin gene in Thalassiosira pseudonana has a fractal dimension of 2.01. The phosphoenolpyruvate carboxylase PPC1 and PPC2 in T. pseudonana were found to have fractal dimensions and CpG dinucleotide content similar to that of P. tricornutum. The fractal dimension of the dnaB replication helicase gene is about 1.98 for both diatoms as well as for the alga Heterosigma akashiwo. In comparison, the E. coli dnaB gene has a fractal dimension of about 2.03. Given that high fractal dimension and CpG dinucleotide content sequences have been associated with the presence of selective pressures, the relatively low fractal dimension gene sequences of the two unique properties of Earth-bound diatoms (photosynthesis and bio-silica cell wall) suggests the potential for the development of high fractal dimension sequences for adaptation in harsh environments.

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Todd Holden, P. Marchese, G. Tremberger Jr., E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, M. Huerta, D. Lieberman, and T. Cheung "Phaeodactylum tricornutum photosynthesis and Thalassiosira pseudonana bio-silica formation genes nucleotide fluctuations", Proc. SPIE 7097, Instruments, Methods, and Missions for Astrobiology XI, 70970R (28 August 2008); https://doi.org/10.1117/12.794414

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KEYWORDS

Fractal analysis

Photosynthesis

Proteins

Calibration

Organisms

Bioinformatics

Cadmium sulfide

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