LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life
Section snippets
Introduction: choosing a character to determine the status of the universal ancestor and ancestors of major phyletic lineages
The nature of the last universal common ancestor (LUCA) i.e. the entity from which all organisms of the Earth would derive, has not yet been clarified. There are studies that indicate that it was a complete cell (genote) (Ouzounis and Kyrpides, 1996; Gogarten, 1995; Lazcano, 1995; Mushegian and Koonin, 1996; Ranea et al., 2006; Ouzounis et al., 2006; Delaye et al., 2002, 2005; Becerra et al., 2007; Mat et al., 2008; Tuller et al., 2010; Méheust et al., 2019). For example, although Méheust et
Materials and methods
To know how the agmatidine synthetase and lysidine synthetase are distributed in the main phyletic lineages, I used several search options available at the www.ncbi.nlm.nih.gov/site. In particular, I used - as a protein database - the Protein option and the logical operators AND, NOT, and OR and, for example, the terms BACTERIA, ARCHAEA, and EUKARYOTA to see which and how many organisms were in possession of these synthetases catalysing the reactions leading to agmatidine and lysidine.
Phylogenetic distribution of the modification of the position 34 of the anticodon in the tRNAIle leading to the evolution of lysidine in bacteria, agmatidine in archaea and inosine in eukaryotes
Reading the AUA codon is a difficult task for organisms because AUA codes for isoleucine (Ile) whereas AUG codes for methionine (Met) (Suzuki and Numata, 2014). This difficulty has been solved in archaea, bacteria and eukaryotes using completely independent but similar evolutionary strategies (Mandal et al., 2010; Suzuki and Numata, 2014). To read the AUA codon, archaea modify the base 34 of the anticodon of a tRNAIle to 2- agmatinylcytidine (agm2C or agmatidine), whereas the bacteria change
The different modifications of the base 34 of the anticodon of a tRNAIle in archaea, bacteria and eukaryotes identify the LUCA and the ancestors of these phyletic lineages as progenotes
The presence of different mechanisms for the recognition of AUA codon based on the evolution of lysidine in bacteria, agmatidine in archaea and inosine in eukaryotes (Muramatsu et al., 1988; Senger et al., 1997; Mandal et al., 2010; Suzuki and Numata, 2014; Nilsson and Alexander, 2019) would testify that these mechanisms emerged only after these phyletic lineages were separated. Otherwise, if they had emerged earlier, these mechanisms would be “identical” or at least not as dissimilar as they
The number of fundamental types of primary cells, i.e. the cellular domains of life, present on earth might be greater than three
The conclusion that LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes might have implications for the number of cellular domains, i.e. the number of basic types of primary cells present on our planet. In fact, if the ancestor of archaea, that of bacteria and that of eukaryotes had been different progenotes (Di Giulio, 2011, 2018), as corroborated here, then the real cells - and not protocells - would have appeared only after the stage of these ancestors. If at
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The time of appearance of the genetic code
2024, BioSystemsThe RNase P, LUCA, the ancestors of the life domains, the progenote, and the tree of life
2022, BioSystemsCitation Excerpt :This way of interpreting multiple alignments (Di Giulio, 2006; 2008b) appears to be compatible with independent observations regarding LUCA, that is with: (i) its high translation errors (Di Giulio, 2021a); (ii) the late appearance of DNA (Di Giulio, 2021b); (iii) the reading mechanism of the AUG and AUA codons (Di Giulio, 2020c); and (iv) the phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNAGln amidotransferase (Di Giulio, 2020b). All this, together with what is reported in the literature (Woese and Fox, 1977; Woese and Gupta, 1981; Woese, 1987, 1998; Doolittle and Brown, 1994; Di Giulio, 1999, 2000, 2001, 2006, 2008a, 2008b, 2008c, 2010, 2011, 2013a, 2013b, 2014, 2015, 2017, 2018, 2019a, 2019b, 2020a, 2020b, 2020c, 2021a, 2021b, 2021c; Anantharaman et al., 2002; Harris et al., 2003; Kim and Caetano-Anollés, 2011; Staley, 2017; de Farias et al., 2021), would also make it plausible the hypothesis that at least LUCA might have been a progenote. Here, I analyse the phylogenetic distribution of a ribonucleoprotein, the RNase P (Phan et al., 2021), in the hope that this being a ribozyme it can provide information about the transition from the RNA world to the world in which catalysis was mediated only from proteins.
The phylogenetic distribution of the cell division system would not imply a cellular LUCA but a progenotic LUCA
2021, BioSystemsCitation Excerpt :Consistent with this interpretation, it is the hypothesis that FtsA could have replaced SepF in bacteria (Pende et al., 2021), which would reinforce the hypothesis that there was a progenotic state at least for LUCA because a replacement of a protein is not expected, or at least unlikely, if we had been in the presence of a cellular stage of LUCA but natural in the case of a progenote (Di Giulio, 2011, 2019a, 2020, 2020a, 2020b, 2021). Indeed, such a massive loss of SepF in bacteria (Pende et al., 2021) is more easily explained by a late progenotic status of the ancestor of bacteria (Di Giulio, 2011, 2020c, 2021). However, more recently it has been shown that a single ancestral gene homolog to the Vpp1 and PspA genes present in bacteria and to the ESCRT-III genes present in eukaryotes and archaea might have been present in LUCA (Liu et al., 2021; Junglas et al., 2021; Kumar Gupta et al., 2021; Deo and Prinz, 2021).
Models of genetic code structure evolution with variable number of coded labels
2021, BioSystemsCitation Excerpt :The early genetic code most likely characterized by a high translational noise, which was further reduced during its evolution (Fitch and Upper, 1987; Barbieri, 2015; Błażej et al., 2019b). Such a state remained likely a long time because the last universal common ancestor of three domains of life, bacteria, archaea and eukaryotes was still a progenote, with not fully developed translational apparatus (Di Giulio, 2001; Giulio, 2014; Di Giulio, 2020a,b). Likewise, amino acids were gradually added to the evolving code.