One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

doi:10.1186/1745-6150-4-4

Biology Direct

Volume 4

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This article is part of a series on Origin and early evolution of life, edited by Dr Eugene V Koonin.

Research

One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

Andrei S Rodin¹ , Eörs Szathmáry²^,3^,4 and Sergei N Rodin²^,5

¹Human Genetics Center, School of Public Health, University of Texas, Houston, TX 77225, USA

²Collegium Budapest (Institute for Advanced Study), Szentháromság u. 2, H-1014 Budapest, Hungary

³Parmenides Center for the Study of Thinking, 14a Kardinal Faulhaber Str., D-80333 München, Germany

⁴Institute of Biology, Eötvös University, 1c Pázmány Péter sétány, H-1117 Budapest, Hungary

⁵Theoretical Biology, Department of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA

author email corresponding author email

Biology Direct 2009, 4:4doi:10.1186/1745-6150-4-4


Published:	27 January 2009

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Additional file 1:

Supplemental figure one. Archaea phylogenetic tree. Halobacterium sp. and Methanosarcina mazei were used as a composite internal outgroup to root the tree. Bootstrap % values are based on 10,000 replications.

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Additional file 2:

Supplemental figure two. Bacteria phylogenetic tree. Halobacterium sp. and Methanothermobacter thermautotrophicus were used as a composite external outgroup to root the tree. Bootstrap % values are based on 10,000 replications. (The 35 species used to reconstruct the tree are the same used by Wolf et al in [21]. The full tree incorporating the sequences from 132 Bacteria species present in [18] is available from the authors upon request).

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Additional file 3:

Supplemental figure three. "Condensed" Bacteria phylogenetic tree. The internal tree branches not supported by bootstrap (i.e. with the bootstrap values less than 50%) were collapsed, resulting in multifurcations. This "condensed" tree topology was robust with respect to the phylogenetic reconstruction method and substitution model.

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Additional file 4:

Supplemental figure four. Eukarya phylogenetic tree. Halobacterium sp. and Methanothermobacter thermautotrophicus were used as a composite external outgroup to root the tree. Bootstrap % values are based on 10,000 replications.

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Additional file 5:

Supplemental figure five. One of the plausible models of elongation of the ancestral palindrome (see Fig. 5 in the text) to the tRNA cloverleaf. The model is based on duplications by self-priming and self-templating. The final cloverleaf has many of the sites of splitting tRNAs on minigenes in archaeal parasite Nanoarchaeum equitance 50 51, as well as the positions of processing in permuted tRNA genes from red algae Cyanidioschyzon merolae 52.

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