The two hypotheses differ about the number and nature of
partners involved in the association; but both support a
chimerical eukaryotic genome and rely on metabolic
interactions that are still widespread in nature. Both assume
that the archaeal partners were methanogens and that
the alphaproteobacteria at the origin of mitochondria were
initially anaerobic. According to these two hypotheses, the
acquisition of chloroplasts would have occurred as described
above. Other associations between bacteria and archaea have
been hypothesised, for example, by Lynn Margulis.
4.3.3 Eukaryotes and Archaea Evolved
from Actinobacteria
Tom Cavalier-Smith (2002) suggested that Archaea and
Eucarya have evolved from an actinobacterium. According
to this author, this scenario is justified by a number of
characteristics shared by actinobacteria, archaea and
eukaryotes (a single membrane cell envelope instead of
two as in most other bacteria, histone H1 and proteasome,
for example). This scenario is attractive because it takes into
account a number of observations. However, it is very controversial because it is:
1. Based on unproven assumptions. It assumes, for example,
that the ancestral state is a two-membraned cell and that
the loss of the outer membrane occurred only once.
2. Based on the subjective choice of a few characteristics
to the exclusion of many others.
3. Not without exceptions (e.g. histone H1 is found today
in some actinobacteria and eukaryotes only).
The scenario thus implies that H1 histones evolved in the
common ancestor of actinobacteria, archaea and eukaryotes
and were then lost in archaea.
4.3.4 Evolution by Simplification
in Microorganisms
Although general trends towards simplification or complexity increase can be identified in some lineages, this
does not mean that such trends can be generalised over
time and over all structures of the lineages under consideration (Brinkmann and Philippe 2005). For example, if the
eukaryotic cell is derived from a prokaryotic cell, this transition was probably accompanied by a phase of increased
complexity in the eukaryotic evolutionary lineage (appearance of membrane compartments, transcription and translation uncoupling, appearance of eukaryotic-specific
multiprotein structures, etc.). This does not mean that this
trend has continued until today in all eukaryotic lineages.
Similarly, changes in prokaryotic lineages should not be
seen as a move towards simplification. Changes within
whatever evolutionary lineage should be seen rather as
alternating phases of simplification and complexity increase
of structures. Simplifying a structure can even coexist with
increase in complexity of another.
Formal evidence of evolution by simplification was
provided by molecular phylogeny and confirmed by comparative genomics. A first example is given by mycoplasma,
very small (2.2–0.8 mm) parasitic bacteria of eukaryotic
cells that are devoid of a cell wall and have genomes
consisting of 500–1,500 kilobases (kb). The genome of
Mycoplasma genitalium (causing severe urinary disorders
in humans) contains only 580 kb corresponding to 480
genes. Because of the small size of their genomes,
mycoplasmas were initially considered as unsophisticated,
‘primitive’ prokaryotes. It is now clear that the small size of
the genome of Mycoplasma genitalium is the result of a
massive loss of genes in relation to its adaptation to a
parasitic lifestyle including loss of the cell wall and a sharp
reduction in its metabolic capacity. A similar phenomenon
has been demonstrated for Buchnera, gammaproteobacterial
symbionts of aphids. Different genes are lost in the case of
Mycoplasma and in the case of Buchnera. This implies that
there are different evolutionary pathways that may be
associated with genomic reduction, each reflecting adaptation to different lifestyles (McCutcheon and Moran 2012).
Another example of evolution by simplification is given
by Archezoa, a polyphyletic assemblage of unicellular
eukaryotes (Diplomonads, Trichomonads and Microsporidia). Archezoa do not synthesise their ATP through
mitochondrial respiration as most eukaryotic cells do
because they do not have mitochondria. This feature, combined with their putative branching at the base of the eukaryotic tree (derived from analysis of the sequences of their
rRNA in the 1980s), was initially interpreted as the fact that
Archezoa were representatives of ancient eukaryotic
lineages that diverged before mitochondrial endosymbiosis.
However, several genes homologous to genes of alphaproteobacterial origin whose products function in mitochondria
in most eukaryotes have been identified in the genomes of
these organisms. One of them is the gene coding for the
synthesis of proteins called ‘heat shock protein 70’ (Hsp70).
These proteins have been visualised in the microsporidian
Trachipleistophora hominis by using specific antibodies and
are concentrated within intracellular vesicles measuring
50–90 nm, surrounded by a double membrane, called
mitosomes* (Williams et al. 2002). Similar vesicles were
also identified in the Diplomonad Giardia intestinalis (pathogenic agent of an intestinal disease called giardiasis) and in
other microsporidia. In Trichomonads such as Trichomonas
vaginalis, genes of mitochondrial origin have been detected
in other cell structures called hydrogenosomes*. Hydrogenosomes are cellular compartments surrounded by a
double membrane, which produce ATP and dihydrogen by
100
J.-C. Bertrand et al.
partners involved in the association; but both support a
chimerical eukaryotic genome and rely on metabolic
interactions that are still widespread in nature. Both assume
that the archaeal partners were methanogens and that
the alphaproteobacteria at the origin of mitochondria were
initially anaerobic. According to these two hypotheses, the
acquisition of chloroplasts would have occurred as described
above. Other associations between bacteria and archaea have
been hypothesised, for example, by Lynn Margulis.
4.3.3 Eukaryotes and Archaea Evolved
from Actinobacteria
Tom Cavalier-Smith (2002) suggested that Archaea and
Eucarya have evolved from an actinobacterium. According
to this author, this scenario is justified by a number of
characteristics shared by actinobacteria, archaea and
eukaryotes (a single membrane cell envelope instead of
two as in most other bacteria, histone H1 and proteasome,
for example). This scenario is attractive because it takes into
account a number of observations. However, it is very controversial because it is:
1. Based on unproven assumptions. It assumes, for example,
that the ancestral state is a two-membraned cell and that
the loss of the outer membrane occurred only once.
2. Based on the subjective choice of a few characteristics
to the exclusion of many others.
3. Not without exceptions (e.g. histone H1 is found today
in some actinobacteria and eukaryotes only).
The scenario thus implies that H1 histones evolved in the
common ancestor of actinobacteria, archaea and eukaryotes
and were then lost in archaea.
4.3.4 Evolution by Simplification
in Microorganisms
Although general trends towards simplification or complexity increase can be identified in some lineages, this
does not mean that such trends can be generalised over
time and over all structures of the lineages under consideration (Brinkmann and Philippe 2005). For example, if the
eukaryotic cell is derived from a prokaryotic cell, this transition was probably accompanied by a phase of increased
complexity in the eukaryotic evolutionary lineage (appearance of membrane compartments, transcription and translation uncoupling, appearance of eukaryotic-specific
multiprotein structures, etc.). This does not mean that this
trend has continued until today in all eukaryotic lineages.
Similarly, changes in prokaryotic lineages should not be
seen as a move towards simplification. Changes within
whatever evolutionary lineage should be seen rather as
alternating phases of simplification and complexity increase
of structures. Simplifying a structure can even coexist with
increase in complexity of another.
Formal evidence of evolution by simplification was
provided by molecular phylogeny and confirmed by comparative genomics. A first example is given by mycoplasma,
very small (2.2–0.8 mm) parasitic bacteria of eukaryotic
cells that are devoid of a cell wall and have genomes
consisting of 500–1,500 kilobases (kb). The genome of
Mycoplasma genitalium (causing severe urinary disorders
in humans) contains only 580 kb corresponding to 480
genes. Because of the small size of their genomes,
mycoplasmas were initially considered as unsophisticated,
‘primitive’ prokaryotes. It is now clear that the small size of
the genome of Mycoplasma genitalium is the result of a
massive loss of genes in relation to its adaptation to a
parasitic lifestyle including loss of the cell wall and a sharp
reduction in its metabolic capacity. A similar phenomenon
has been demonstrated for Buchnera, gammaproteobacterial
symbionts of aphids. Different genes are lost in the case of
Mycoplasma and in the case of Buchnera. This implies that
there are different evolutionary pathways that may be
associated with genomic reduction, each reflecting adaptation to different lifestyles (McCutcheon and Moran 2012).
Another example of evolution by simplification is given
by Archezoa, a polyphyletic assemblage of unicellular
eukaryotes (Diplomonads, Trichomonads and Microsporidia). Archezoa do not synthesise their ATP through
mitochondrial respiration as most eukaryotic cells do
because they do not have mitochondria. This feature, combined with their putative branching at the base of the eukaryotic tree (derived from analysis of the sequences of their
rRNA in the 1980s), was initially interpreted as the fact that
Archezoa were representatives of ancient eukaryotic
lineages that diverged before mitochondrial endosymbiosis.
However, several genes homologous to genes of alphaproteobacterial origin whose products function in mitochondria
in most eukaryotes have been identified in the genomes of
these organisms. One of them is the gene coding for the
synthesis of proteins called ‘heat shock protein 70’ (Hsp70).
These proteins have been visualised in the microsporidian
Trachipleistophora hominis by using specific antibodies and
are concentrated within intracellular vesicles measuring
50–90 nm, surrounded by a double membrane, called
mitosomes* (Williams et al. 2002). Similar vesicles were
also identified in the Diplomonad Giardia intestinalis (pathogenic agent of an intestinal disease called giardiasis) and in
other microsporidia. In Trichomonads such as Trichomonas
vaginalis, genes of mitochondrial origin have been detected
in other cell structures called hydrogenosomes*. Hydrogenosomes are cellular compartments surrounded by a
double membrane, which produce ATP and dihydrogen by
100
J.-C. Bertrand et al.