Limits...
The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Bottom Line: This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway.Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase.These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

View Article: PubMed Central - PubMed

Affiliation: Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur , Paris, France ; Institut de Biologie Intégrative de la cellule, Université Paris-Saclay , Paris, France.

ABSTRACT
Biologists used to draw schematic "universal" trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese's universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

No MeSH data available.


Related in: MedlinePlus

Evolution of the biosynthesis pathway of threonylcarbamoyl adenosine (t6A) from LUCA to the three domains of life. Homologous proteins have the same shapes and colors, except for YgjE and YeaZ, which are homologous but not orthologous. In this scenario, this universal tRNA modification was performed in LUCA by two universal proteins (the ancestors of Kae1/YgjD and of Sua5/YrdC, respectively), as in mitochondria (Wan et al., 2013; Thiaville et al., 2014). Additional proteins are now essential for t6A synthesis in modern organisms (Deutsch et al., 2012; Perrochia et al., 2013a,b). The bacterial proteins (YjeE, YeaZ) are non-homologous to the archaeal/eukaryal ones (Bud32, Pcc1, Cgi121). The most parsimonious scenario supports the rooting between Bacteria and Archaea/Eukarya, because other roots would require the presence of the Bud32, Pcc1, and Cgi121 proteins in LUCA, and their replacement by the YeaZ, YjeE proteins in Bacteria, an unlikely evolutionary pathway (see text).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4508532&req=5

Figure 2: Evolution of the biosynthesis pathway of threonylcarbamoyl adenosine (t6A) from LUCA to the three domains of life. Homologous proteins have the same shapes and colors, except for YgjE and YeaZ, which are homologous but not orthologous. In this scenario, this universal tRNA modification was performed in LUCA by two universal proteins (the ancestors of Kae1/YgjD and of Sua5/YrdC, respectively), as in mitochondria (Wan et al., 2013; Thiaville et al., 2014). Additional proteins are now essential for t6A synthesis in modern organisms (Deutsch et al., 2012; Perrochia et al., 2013a,b). The bacterial proteins (YjeE, YeaZ) are non-homologous to the archaeal/eukaryal ones (Bud32, Pcc1, Cgi121). The most parsimonious scenario supports the rooting between Bacteria and Archaea/Eukarya, because other roots would require the presence of the Bud32, Pcc1, and Cgi121 proteins in LUCA, and their replacement by the YeaZ, YjeE proteins in Bacteria, an unlikely evolutionary pathway (see text).

Mentions: Recent biochemical work in our laboratory exemplifies why comparative biochemistry data support a universal tree in Archaea and Eukarya are indeed sister domains. Several research groups, as well as our team in Orsay, succeeded in reconstituting in vitro the protein complexes involved in the biosynthesis of the universal threonylcarbamoyl adenosine (t6A) tRNA modification in position 37 of tRNA in the three domains of life (Deutsch et al., 2012; Perrochia et al., 2013a,b) and in mitochondria (Wan et al., 2013; Thiaville et al., 2014). In Bacteria, Archaea and Eukarya, the reactions require the combination of two universal proteins and essential accessory proteins that exist in two versions, one present in Bacteria, the other present in Archaea and Eukarya. Interestingly, the same reaction can be performed in mitochondria by the two universal proteins alone, one (Qri7) that came from Bacteria via the endosymbiotic route and the other (Kae1) corresponding to the eukaryotic version (Wan et al., 2013; Thiaville et al., 2014). These results suggest that LUCA was able to perform this universally conserved reaction with the ancestors of the two universal proteins and that accessory proteins (now essential) were added independently in the bacterial and in the archaeal/eukaryal lineages. The most parsimonious scenario, illustrated in Figure 2, supports the rooting between Bacteria and Archaea/Eukarya, because other roots would require the presence of the archaeal/eukaryal set of accessory proteins in LUCA, and its replacement by the non-homologous bacterial set in Bacteria. This seems unlikely because biochemical analyses have shown that the bacterial and archael/eukaryal accessory proteins are not functionally equivalent (Deutsch et al., 2012; Perrochia et al., 2013b). It is therefore difficult to imagine intermediate steps in the replacement process. Furthermore, such replacement, even partial, never occurred during the diversification of the three domains.


The universal tree of life: an update.

Forterre P - Front Microbiol (2015)

Evolution of the biosynthesis pathway of threonylcarbamoyl adenosine (t6A) from LUCA to the three domains of life. Homologous proteins have the same shapes and colors, except for YgjE and YeaZ, which are homologous but not orthologous. In this scenario, this universal tRNA modification was performed in LUCA by two universal proteins (the ancestors of Kae1/YgjD and of Sua5/YrdC, respectively), as in mitochondria (Wan et al., 2013; Thiaville et al., 2014). Additional proteins are now essential for t6A synthesis in modern organisms (Deutsch et al., 2012; Perrochia et al., 2013a,b). The bacterial proteins (YjeE, YeaZ) are non-homologous to the archaeal/eukaryal ones (Bud32, Pcc1, Cgi121). The most parsimonious scenario supports the rooting between Bacteria and Archaea/Eukarya, because other roots would require the presence of the Bud32, Pcc1, and Cgi121 proteins in LUCA, and their replacement by the YeaZ, YjeE proteins in Bacteria, an unlikely evolutionary pathway (see text).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508532&req=5

Figure 2: Evolution of the biosynthesis pathway of threonylcarbamoyl adenosine (t6A) from LUCA to the three domains of life. Homologous proteins have the same shapes and colors, except for YgjE and YeaZ, which are homologous but not orthologous. In this scenario, this universal tRNA modification was performed in LUCA by two universal proteins (the ancestors of Kae1/YgjD and of Sua5/YrdC, respectively), as in mitochondria (Wan et al., 2013; Thiaville et al., 2014). Additional proteins are now essential for t6A synthesis in modern organisms (Deutsch et al., 2012; Perrochia et al., 2013a,b). The bacterial proteins (YjeE, YeaZ) are non-homologous to the archaeal/eukaryal ones (Bud32, Pcc1, Cgi121). The most parsimonious scenario supports the rooting between Bacteria and Archaea/Eukarya, because other roots would require the presence of the Bud32, Pcc1, and Cgi121 proteins in LUCA, and their replacement by the YeaZ, YjeE proteins in Bacteria, an unlikely evolutionary pathway (see text).
Mentions: Recent biochemical work in our laboratory exemplifies why comparative biochemistry data support a universal tree in Archaea and Eukarya are indeed sister domains. Several research groups, as well as our team in Orsay, succeeded in reconstituting in vitro the protein complexes involved in the biosynthesis of the universal threonylcarbamoyl adenosine (t6A) tRNA modification in position 37 of tRNA in the three domains of life (Deutsch et al., 2012; Perrochia et al., 2013a,b) and in mitochondria (Wan et al., 2013; Thiaville et al., 2014). In Bacteria, Archaea and Eukarya, the reactions require the combination of two universal proteins and essential accessory proteins that exist in two versions, one present in Bacteria, the other present in Archaea and Eukarya. Interestingly, the same reaction can be performed in mitochondria by the two universal proteins alone, one (Qri7) that came from Bacteria via the endosymbiotic route and the other (Kae1) corresponding to the eukaryotic version (Wan et al., 2013; Thiaville et al., 2014). These results suggest that LUCA was able to perform this universally conserved reaction with the ancestors of the two universal proteins and that accessory proteins (now essential) were added independently in the bacterial and in the archaeal/eukaryal lineages. The most parsimonious scenario, illustrated in Figure 2, supports the rooting between Bacteria and Archaea/Eukarya, because other roots would require the presence of the archaeal/eukaryal set of accessory proteins in LUCA, and its replacement by the non-homologous bacterial set in Bacteria. This seems unlikely because biochemical analyses have shown that the bacterial and archael/eukaryal accessory proteins are not functionally equivalent (Deutsch et al., 2012; Perrochia et al., 2013b). It is therefore difficult to imagine intermediate steps in the replacement process. Furthermore, such replacement, even partial, never occurred during the diversification of the three domains.

Bottom Line: This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway.Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase.These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

View Article: PubMed Central - PubMed

Affiliation: Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur , Paris, France ; Institut de Biologie Intégrative de la cellule, Université Paris-Saclay , Paris, France.

ABSTRACT
Biologists used to draw schematic "universal" trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese's universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

No MeSH data available.


Related in: MedlinePlus