Polyphasic evidence delineating the root of life and roots of biological domains

Wong, J. Tze‐Fei; Chen, Jian‐Huan; Mat, Wai‐Kin; Ng, Siu-Kin; Xue, Hong

doi:10.1016/j.gene.2007.07.032

Cited by 37 publications

(34 citation statements)

References 90 publications

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“…This is compatible with the suggestion that methanogenesis is a very early pathway in the history of life (Brocks et al, 1999;Battistuzzi et al, 2004;Bapteste et al, 2005;Ueno et al, 2006). Finally, this observation also corroborates the hypothesis that the LUCA was a methanogen (Xue et al, 2005;Wong et al, 2007).…”

Section: Discussionsupporting

confidence: 91%

A methanogen hosted the origin of the genetic code

Giulio

2009

Journal of Theoretical Biology

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A c c e p t e d m a n u s c r i p t A c c e p t e d m a n u s c r i p t 2 AbstractA comparison is made between orthologous proteins from a methanogen (Methanopyrus kandleri) and from a non-methanogen (Pyrococcus abyssi) in order to determine the amino acid substitution pattern. This analysis makes it possible to establish which amino acids are significantly and asymmetrically utilised by these two organisms. A methanophily index (MI) based on this asymmetry makes it possible for any protein to be associated with a numerical value which, when calculated for the same orthologous protein from methanogenic and nonmethanogenic organisms, turns out to have the power to discriminate between these two groups of organisms, even if only for about 20% of the analysed proteins. The MI can also be associated to the genetic code under the assumption that the frequency of synonymous codons specifying the amino acids in the genetic code also reflects the frequency with which amino acids appeared in ancestral proteins. Finally a t test shows that the MI value associated to the genetic code is not different from the mean value of the MI deriving from methanogen proteins, but it differs from the mean MI of non-methanogen proteins. This might indicate that the genetic code evolved in a methanogenic 'organism'.

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Section: Discussionsupporting

confidence: 91%

A methanogen hosted the origin of the genetic code

Giulio

2009

Journal of Theoretical Biology

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“…3, see also Lineweaver and Schwartzman, 2005;Wong et al, 2007). Extant organisms with the shortest branches are hyperthermophiles able to tolerate temperatures above 90°C.…”

Section: Hyperthermophilia and The Deepest Branches Of Terrestrial Lifementioning

confidence: 99%

“…Plants, animals and fungi are represented in the lower left by Zea (Corn), Homo (humans) and Coprinus (mushrooms) respectively. The position of the root is from ancient gene duplication studies (Iwabe et al, 1989;Brown and Doolittle, 1995;Wong et al, 2007;Gaucher et al, 2010). Numbered nodes are described in Figure 4 and Table 1.…”

Section: Hyperthermophilia and The Deepest Branches Of Terrestrial Lifementioning

confidence: 99%

What Can Life on Earth Tell Us About Life in the Universe?

Lineweaver

Chopra

2012

Cellular Origin, Life in Extreme Habitats and Astrobiology

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“…It has been argued that the tRNA set of the archaeon Methanopyrus kandleri reflects a relatively early stage of development and resembles that in the LUCA (Tong and Wong 2004;Wong et al 2007; but see Brochier et al 2004). In accord with the scenario developed here, the tRNA set of M. kandleri resembles the 20 tRNA set depicted in the left panel of Fig.…”

Section: A Set Of 20 Trnas Able To Translate All 20 Amino Acidsmentioning

confidence: 99%