genitalium and Haemophilus influenzae (genomes of
0.58 Mb for 468 genes and 1.83 Mb for 1,700 genes, respectively) that have diverged from a common ancestor probably
more than 1.5 billion years ago (Mushegian and Koonin
1996). This approach identified 256 conserved genes in
both bacteria, supposedly close to the minimum number
necessary for the maintenance of cellular life. It is important
to note that this number is similar to those obtained by the
experimental methods described above. In particular, the
minimal genome contains:
1. The DNA replication machinery
2. A rudimentary system for DNA repair and recombination
3. An almost complete transcription system but without
regulatory factors
4. Chaperones
5. An anaerobic intermediary metabolism restricted to
glycolysis
6. No system for the synthesis of amino acids and
nucleotides
7. A limited biosynthetic pathway of lipids (no fatty acid
synthesis)
8. A protein export system
9. A limited repertoire of proteins for the transport of
metabolites
The nutritional needs of such a cell are quite large: it
would need to import all of its amino acids, nucleotides, fatty
acids and coenzyme complexes.
One limitation of this study is that the inferred genome is
probably closer to that present in the last ancestor of bacteria than to the genome of LUCA. Since this analysis
compares two bacterial genomes, it is very likely that this
minimal genome contains bacterial solutions for some
functions (such as a system of DNA replication of bacterial
type; cf. Sects. 4.1.4 and 4.1.5). For example, the same
study applied to 21 genomes of Bacteria and Archaea led
to a list of only 52 genes encoding mainly for proteins
involved in the formation of the ribosome and in protein
biosynthesis.
Therefore, a less restrictive approach has been proposed. It is based on the search for universally conserved
functions (which may have been present in LUCA) rather
than on the search for universally conserved homologous
genes. This search suggests a universal common ancestor
with only 500–600 genes. The resulting cell could de
novo synthesise its amino acids, nucleotides, complex
carbohydrates and some coenzymes and would depend
only on a small number of precursors taken from the
environment (Koonin 2003).
All these studies show that the genome of LUCA probably contained at least a few hundred genes and corresponds
to that of a relatively modern cell (i.e. ensuring functions
similar to those currently observed).
4.1.6 LUCA: Hyperthermophilic, Thermophilic
or Mesophilic?
Another discussion point concerns the optimal growth temperature of LUCA. The question is whether the ability to live
at high temperatures is a character acquired early or late
during evolution. The temperature at which LUCA lived is
often confused with the temperature at which life emerged.
These issues must clearly be separated because LUCA and
the emergence of life are two separate events in time and
space (Fig. 4.2). Currently, the majority of known hyperthermophilic organisms (living above 80–85
C) are Archaea.
There are also hyperthermophilic bacteria such as
Thermotogales and Aquificales. However, no eukaryotic
organism able to live above 60–65
C is currently known.
The first school of thought, championed by Carl Woese,
Karl Stetter and Norman Pace, considers that LUCA was a
hyperthermophilic organism (Stetter 2006). This hypothesis
is based mainly on the fact that hyperthermophilic organisms
occupy a basal position within the bacterial and archaeal
domains in the universal tree of life based on the small
subunit ribosomal RNA and rooted in the bacterial branch
(see Sect. 6.6.2). Moreover, these microorganisms are
associated with shorter branches than those associated with
mesophilic (living below 60
C) or thermophilic (living
between 60 and 80
C) microorganisms. These two
observations have been interpreted as indicating an ancient
origin and a slower evolutionary rate of these
microorganisms, which are therefore likely to have retained
a large number of traits inherited from LUCA, in particular
hyperthermophily. The ability to live in mesophilic
environments would therefore have appeared secondarily
and independently in the three domains of life.
Although the idea of a hyperthermophilic LUCA is generally taught, it is disputed by some scientists who believe that
LUCA was not hyperthermophilic and that the adaptation to
extremely hot environments observed in extant organisms
appeared secondarily (Forterre et al. 2000). For example, the
analysis of the most evolutionarily conserved parts of ribosomal RNA genes suggests that the basal emergence of both
hyperthermophilic bacterial phyla could be an artefact of the
tree reconstruction artefact rather than a reflection of their
evolutionary origin (Brochier and Philippe 2002).
The hypothesis of a mesophilic LUCA is reinforced by
results obtained by Galtier and colleagues (1999) who estimated
the composition in G or C bases of the ribosomal RNA of
LUCA by statistical methods. Knowing that stable RNAs
(rRNA, tRNA) are rich in G and C in hyperthermophiles,
these authors concluded that LUCA could not have survived
temperatures above 70
C. Further work on rRNAs and
universal proteins has confirmed and expanded these results
(Boussau et al. 2008). It seems that LUCA was mesophilic
82
J.-C. Bertrand et al.
0.58 Mb for 468 genes and 1.83 Mb for 1,700 genes, respectively) that have diverged from a common ancestor probably
more than 1.5 billion years ago (Mushegian and Koonin
1996). This approach identified 256 conserved genes in
both bacteria, supposedly close to the minimum number
necessary for the maintenance of cellular life. It is important
to note that this number is similar to those obtained by the
experimental methods described above. In particular, the
minimal genome contains:
1. The DNA replication machinery
2. A rudimentary system for DNA repair and recombination
3. An almost complete transcription system but without
regulatory factors
4. Chaperones
5. An anaerobic intermediary metabolism restricted to
glycolysis
6. No system for the synthesis of amino acids and
nucleotides
7. A limited biosynthetic pathway of lipids (no fatty acid
synthesis)
8. A protein export system
9. A limited repertoire of proteins for the transport of
metabolites
The nutritional needs of such a cell are quite large: it
would need to import all of its amino acids, nucleotides, fatty
acids and coenzyme complexes.
One limitation of this study is that the inferred genome is
probably closer to that present in the last ancestor of bacteria than to the genome of LUCA. Since this analysis
compares two bacterial genomes, it is very likely that this
minimal genome contains bacterial solutions for some
functions (such as a system of DNA replication of bacterial
type; cf. Sects. 4.1.4 and 4.1.5). For example, the same
study applied to 21 genomes of Bacteria and Archaea led
to a list of only 52 genes encoding mainly for proteins
involved in the formation of the ribosome and in protein
biosynthesis.
Therefore, a less restrictive approach has been proposed. It is based on the search for universally conserved
functions (which may have been present in LUCA) rather
than on the search for universally conserved homologous
genes. This search suggests a universal common ancestor
with only 500–600 genes. The resulting cell could de
novo synthesise its amino acids, nucleotides, complex
carbohydrates and some coenzymes and would depend
only on a small number of precursors taken from the
environment (Koonin 2003).
All these studies show that the genome of LUCA probably contained at least a few hundred genes and corresponds
to that of a relatively modern cell (i.e. ensuring functions
similar to those currently observed).
4.1.6 LUCA: Hyperthermophilic, Thermophilic
or Mesophilic?
Another discussion point concerns the optimal growth temperature of LUCA. The question is whether the ability to live
at high temperatures is a character acquired early or late
during evolution. The temperature at which LUCA lived is
often confused with the temperature at which life emerged.
These issues must clearly be separated because LUCA and
the emergence of life are two separate events in time and
space (Fig. 4.2). Currently, the majority of known hyperthermophilic organisms (living above 80–85
C) are Archaea.
There are also hyperthermophilic bacteria such as
Thermotogales and Aquificales. However, no eukaryotic
organism able to live above 60–65
C is currently known.
The first school of thought, championed by Carl Woese,
Karl Stetter and Norman Pace, considers that LUCA was a
hyperthermophilic organism (Stetter 2006). This hypothesis
is based mainly on the fact that hyperthermophilic organisms
occupy a basal position within the bacterial and archaeal
domains in the universal tree of life based on the small
subunit ribosomal RNA and rooted in the bacterial branch
(see Sect. 6.6.2). Moreover, these microorganisms are
associated with shorter branches than those associated with
mesophilic (living below 60
C) or thermophilic (living
between 60 and 80
C) microorganisms. These two
observations have been interpreted as indicating an ancient
origin and a slower evolutionary rate of these
microorganisms, which are therefore likely to have retained
a large number of traits inherited from LUCA, in particular
hyperthermophily. The ability to live in mesophilic
environments would therefore have appeared secondarily
and independently in the three domains of life.
Although the idea of a hyperthermophilic LUCA is generally taught, it is disputed by some scientists who believe that
LUCA was not hyperthermophilic and that the adaptation to
extremely hot environments observed in extant organisms
appeared secondarily (Forterre et al. 2000). For example, the
analysis of the most evolutionarily conserved parts of ribosomal RNA genes suggests that the basal emergence of both
hyperthermophilic bacterial phyla could be an artefact of the
tree reconstruction artefact rather than a reflection of their
evolutionary origin (Brochier and Philippe 2002).
The hypothesis of a mesophilic LUCA is reinforced by
results obtained by Galtier and colleagues (1999) who estimated
the composition in G or C bases of the ribosomal RNA of
LUCA by statistical methods. Knowing that stable RNAs
(rRNA, tRNA) are rich in G and C in hyperthermophiles,
these authors concluded that LUCA could not have survived
temperatures above 70
C. Further work on rRNAs and
universal proteins has confirmed and expanded these results
(Boussau et al. 2008). It seems that LUCA was mesophilic
82
J.-C. Bertrand et al.