Proto-ubiquitin: A Bayesian Prediction of an Ancient Protein During the Prokaryotic-Eukaryotic Transition
Custer C. Deocaris1*, Lovette F. Cunanan2, Richelda A. Galapia2,
and Marla A. Endriga2
1College of Home Economics, University of the Philippines,
Diliman, Quezon City
2Department of Biology, College of Arts and Sciences,
University of the Philippines Manila, Ermita, 1000 Manila, Philippines
corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.
ABSTRACT
Only recently have biologists been able to apply mathematical and biochemical tools to preview lifestyles of ancient life forms and "travel back in time." In this paper, we describe an ancestral reconstruction of ubiquitin to determine its molecular properties during the rise of the eukaryotes. Although ubiquitin is one of the most conserved proteins in eukaryotes, no ubiquitin homolog has been found in prokaryotic genomes sequenced thus far. In an attempt to derive the ancestral ubiquitin, or proto-ubiquitin (proto-Ub), we applied Bayesian statistical theory to estimate posterior probabilities of protein sequences from a minimum evolution tree of 30 extant species. The inferred ancestral sequence was 100% homologous with the ubiquitin of Brugia malayi, a parasitic nematode. Among its 76 amino acids, only nine residues have undergone amino acid modification. As no major structural and functional changes happened during the evolution of ubiquitin, we hypothesize that the stressful conditions that led to the creation of this gene after the "Great Oxidation Event" 2.4 billion years ago may have already been "buffered" to date.
INTRODUCTION
What was Earth like when eukaryotes were just starting to emerge from the oceans? Planetary biologists widely believe that proteotoxic stress from increasing oxygen levels and ocean temperatures around 2 billion (Gyr) years ago prompted the origin of the first eukaryote via endosymbiosis (reviewed recently by Deocaris et al. 2010), and that the steady build-up of oxygen by cyanobacterial photosynthesis helped create the Earth's early atmosphere . . . . . . . . .
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