domains, the importance of which was confirmed by comparative genomics, is discussed in Chap. 12.
Other scenarios may further complicate analyses. For
example, some genes inherited from LUCA may have been
lost in one or more domains. Thus, genes absent in one or
more domains (or even in all extant organisms) may have
existed in LUCA (Fig. 4.4d).
Similarly, genes inherited from LUCA may have been
replaced in one domain. Thus, functions present in
representatives of one or more domains, but due to nonhomologous genes, could have existed in LUCA (Fig. 4.4e).
A final possibility is that nonhomologous genes encoding
proteins with similar functions have appeared independently
in the three domains of life. This is a phenomenon called
evolutionary convergence* (Fig. 4.4f). In fact, very
different molecules may have been independently recruited
to perform similar functions. The flagellum that allows cell
motility is an example of evolution by convergence (for
another example, see the proteins carrying DNA replication,
next section). A flagellum composed of several proteins
exists in the three domains of life, suggesting that a
flagellum was already present in LUCA. However, the
detailed analysis of these flagella in the three domains
revealed they have three very different organisations and
that their constituents are not homologous. The existence
of three types of flagella (one for each domain of life)
can support the hypothesis that LUCA had no flagellum
and that the latter was established independently in the
three domains of life from different components. Alternatively, LUCA could have had one of three types of
flagella that was replaced twice during evolution by new
and different structures performing the same function, cell
motility.
These examples illustrate that the research and analysis of
characteristics common to the three domains is complex. On
this point, the contribution of molecular phylogeny is crucial
because, in reconstructing the evolutionary history of genes,
it has identified which genes are more likely to have been
present in the genome of LUCA. These approaches are
limited in part by our still very fragmented knowledge of
extant organisms and by the fact that the vast majority of
past organisms became extinct without leaving any
descendants or fossils.
4.1.4 The Main Features of LUCA
Despite the significant limitations set forth above, it is possible to sketch a portrait of LUCA. LUCA was a complex
organism with probably:
1. A DNA-based genome. The assumption of a LUCA with a
DNA genome is not universally accepted, though, because
the majority of proteins carrying DNA replication in
Bacteria are not homologous to those of Archaea and
Eucarya. Three explanations have been advanced to
explain the non-homology of these proteins: (a) LUCA
had a DNA genome and proteins carrying DNA replication
were replaced by other proteins in the lineage leading to
Bacteria or in the Archaea/Eucarya ancestor (Fig. 4.4e);
(b) LUCA had an RNA genome and DNA appeared twice,
independently, in the lineages of Bacteria and of Archaea/
Eucarya (Fig. 4.4f); (c) LUCA had an RNA genome and
the transition to DNA from RNA occurred in one of the
domains or in viruses (Fig. 4.1). Genes that carry out DNA
replication and the synthesis of deoxyribonucleotides were
secondarily transferred to other domains, which acquired
the ability to make DNA (Fig. 4.4c).
2. A plasma membrane conforming to the ‘fluid mosaic’
model (cf. Sect. 3.3.1), which implies that LUCA was
probably a cellular organism. The membrane of LUCA
very likely integrated an ATP-generating system
(because of the universal presence of ATPases) and a
system of protein export. The nature of the lipids
constituting the membrane of LUCA is still the subject
of much controversy.
3. A genetic code controlling the translation of RNA into
proteins.
4. Ribosomes, transfer RNAs, aminoacyl tRNA synthetases,
and a number of translation factors involved in protein
synthesis.
Many other issues, such as the presence or absence of introns
and the type of metabolism, are currently being discussed,
but the scientific community has not yet reached a
consensus.
4.1.5 The Genome of LUCA
Another very hotly debated issue regards the number of
genes in the genome of LUCA. There are two opposing
views: the proponents of LUCA with a minimal genome
(i.e. very small, containing few genes) and those arguing
that LUCA had a large genome, containing thousands of
genes. In the first view, the evolution of genomes after
LUCA would be primarily by ‘increasing complexity’
(gene gain, through duplication and/or horizontal gene transfer), whereas in the second view, changes in gene stock
would have been by gene loss. One of the key ideas upon
which the supporters of LUCA with a small genome base
their hypothesis is that the enzymes encoded by early genes
could have had a broader spectrum than those of current
enzymes. This very low specificity could result in a number
of essential enzymes lower than that required for present
microorganisms.
80
J.-C. Bertrand et al.
Other scenarios may further complicate analyses. For
example, some genes inherited from LUCA may have been
lost in one or more domains. Thus, genes absent in one or
more domains (or even in all extant organisms) may have
existed in LUCA (Fig. 4.4d).
Similarly, genes inherited from LUCA may have been
replaced in one domain. Thus, functions present in
representatives of one or more domains, but due to nonhomologous genes, could have existed in LUCA (Fig. 4.4e).
A final possibility is that nonhomologous genes encoding
proteins with similar functions have appeared independently
in the three domains of life. This is a phenomenon called
evolutionary convergence* (Fig. 4.4f). In fact, very
different molecules may have been independently recruited
to perform similar functions. The flagellum that allows cell
motility is an example of evolution by convergence (for
another example, see the proteins carrying DNA replication,
next section). A flagellum composed of several proteins
exists in the three domains of life, suggesting that a
flagellum was already present in LUCA. However, the
detailed analysis of these flagella in the three domains
revealed they have three very different organisations and
that their constituents are not homologous. The existence
of three types of flagella (one for each domain of life)
can support the hypothesis that LUCA had no flagellum
and that the latter was established independently in the
three domains of life from different components. Alternatively, LUCA could have had one of three types of
flagella that was replaced twice during evolution by new
and different structures performing the same function, cell
motility.
These examples illustrate that the research and analysis of
characteristics common to the three domains is complex. On
this point, the contribution of molecular phylogeny is crucial
because, in reconstructing the evolutionary history of genes,
it has identified which genes are more likely to have been
present in the genome of LUCA. These approaches are
limited in part by our still very fragmented knowledge of
extant organisms and by the fact that the vast majority of
past organisms became extinct without leaving any
descendants or fossils.
4.1.4 The Main Features of LUCA
Despite the significant limitations set forth above, it is possible to sketch a portrait of LUCA. LUCA was a complex
organism with probably:
1. A DNA-based genome. The assumption of a LUCA with a
DNA genome is not universally accepted, though, because
the majority of proteins carrying DNA replication in
Bacteria are not homologous to those of Archaea and
Eucarya. Three explanations have been advanced to
explain the non-homology of these proteins: (a) LUCA
had a DNA genome and proteins carrying DNA replication
were replaced by other proteins in the lineage leading to
Bacteria or in the Archaea/Eucarya ancestor (Fig. 4.4e);
(b) LUCA had an RNA genome and DNA appeared twice,
independently, in the lineages of Bacteria and of Archaea/
Eucarya (Fig. 4.4f); (c) LUCA had an RNA genome and
the transition to DNA from RNA occurred in one of the
domains or in viruses (Fig. 4.1). Genes that carry out DNA
replication and the synthesis of deoxyribonucleotides were
secondarily transferred to other domains, which acquired
the ability to make DNA (Fig. 4.4c).
2. A plasma membrane conforming to the ‘fluid mosaic’
model (cf. Sect. 3.3.1), which implies that LUCA was
probably a cellular organism. The membrane of LUCA
very likely integrated an ATP-generating system
(because of the universal presence of ATPases) and a
system of protein export. The nature of the lipids
constituting the membrane of LUCA is still the subject
of much controversy.
3. A genetic code controlling the translation of RNA into
proteins.
4. Ribosomes, transfer RNAs, aminoacyl tRNA synthetases,
and a number of translation factors involved in protein
synthesis.
Many other issues, such as the presence or absence of introns
and the type of metabolism, are currently being discussed,
but the scientific community has not yet reached a
consensus.
4.1.5 The Genome of LUCA
Another very hotly debated issue regards the number of
genes in the genome of LUCA. There are two opposing
views: the proponents of LUCA with a minimal genome
(i.e. very small, containing few genes) and those arguing
that LUCA had a large genome, containing thousands of
genes. In the first view, the evolution of genomes after
LUCA would be primarily by ‘increasing complexity’
(gene gain, through duplication and/or horizontal gene transfer), whereas in the second view, changes in gene stock
would have been by gene loss. One of the key ideas upon
which the supporters of LUCA with a small genome base
their hypothesis is that the enzymes encoded by early genes
could have had a broader spectrum than those of current
enzymes. This very low specificity could result in a number
of essential enzymes lower than that required for present
microorganisms.
80
J.-C. Bertrand et al.