4.1.5.1 The Smallest Known Cellular Genome
The study of the smallest extant prokaryotic genomes has led
to a few estimates of the minimum number of genes that the
genome of a cellular organism may contain and could therefore have been present in the genome of LUCA.
One of the smallest cellular genome known as of today is
that of the endosymbiotic bacterium Carsonella ruddii
(Nakabachi et al. 2006). This is a gammaproteobacterium
that infects all species of psyllid, Hemiptera insects feeding
exclusively on plant sap. Its genome consists of 160
kilobases and contains 182 protein-coding genes. This
genome is also extreme in its base composition: 84 % of A
or T and only 16 % of C or G. Carsonella ruddii depends
very closely on its host since it is completely devoid of genes
involved in the biosynthesis of the membrane and in the
metabolism of lipids and nucleotides. In contrast, the
genome of this symbiont contains a large number of genes
encoding proteins involved in the synthesis of essential
amino acids (~18 % of genes). This symbiont is essential
to the survival of the host insect, which does not find these
amino acids in its single food source. Some authors interpret
this genomic reduction as a process comparable to that
experienced by mitochondrial and chloroplastic genomes.
Others, on the contrary, think that this is an evolutionary
dead end that will ultimately lead to the demise of this
symbiont. More recently, even smaller genomes have been
discovered such as the betaproteobacterium ‘Candidatus
Tremblaya princeps’ (139 kilobases, 121 protein-coding
genes) or the alphaproteobacterium ‘Candidatus Hodgkinia
cicadicola’ (148 kilobases, 169 protein-coding genes)
(McCutcheon and Moran 2012).
In general terms, the smallest sequenced prokaryotic
genomes contain a few hundreds of genes. They come
from symbionts or parasites whose highly specialised ways
of life have led to very intense genome reduction:
Nanoarchaeum equitans in Archaea and Mycoplasma and
Buchnera in Bacteria. The small genome size of these extant
cellular organisms is believed to be the result of recent and
independent genomic reduction events rather than a feature
inherited from a common ancestor.
4.1.5.2 Experimental Approaches
Systematic experiments of in vitro gene inactivation were
used to identify genes essential for maintaining cellular life.
The underlying assumption is that these essential genes
could be inherited from LUCA. The results show that not
all genes of a prokaryotic genome are necessary for the
survival of a cell. For example, of the 480 genes in the
genome of Mycoplasma genitalium, only two-thirds are
actually needed for growth in laboratory. Similarly, in Bacillus subtilis, only 271 of the 4,100 genes present in the
genome have proven essential to the maintenance of cellular
life in the laboratory. In the yeast Saccharomyces cerevisiae,
nearly 1,000 genes are detected as required. Despite significant variation according to the organisms studied and the
experimental methods used to determine the number of
essential genes, a ‘minimal’ cell seems to emerge from
these studies: it is a simple prokaryotic cell consisting of a
compartment defined by a membrane and performing typical
cellular functions:
1. Replication
2. Isolation of the compartment from the outer medium
3. Protein synthesis
4. A rudimentary metabolism for energy production
(glycolysis)
A major limitation of these experiments is that they
involve the inactivation of a single gene at a time. Thus,
the effect of the simultaneous inactivation of several individually dispensable genes is not taken into account (e.g.
two genes can be individually dispensable without being so
simultaneously). For example, the bacterium Escherichia
coli has genes coding for two types of ribonucleoside
diphosphate reductases that catalyse the reduction of ribonucleoside diphosphates into deoxyribonucleoside diphosphates under aerobic conditions and anaerobic conditions,
respectively. Inactivation of the genes encoding the enzyme
operating under aerobic conditions does not prevent the
growth of E. coli under anaerobic conditions. They are
therefore dispensable genes. Similarly, inactivation of
genes encoding the enzyme operating anaerobically does
not prevent the aerobic growth of E. coli. They are therefore
also dispensable genes. However, the simultaneous inactivation of genes encoding the two types of enzymes is lethal.
Finally, we must not forget that these experiments were
conducted in laboratory conditions that are optimal for the
microorganisms studied. The experimenters supplement all
their nutritional requirements; they are neither subjected to
stress nor are they in competition with other microorganisms. While most individual gene inactivation does
not prevent strain growth in the laboratory, microorganisms
that carry one such inactivation, however, are unable to
thrive in a natural environment where the number of essential genes is much more important.
4.1.5.3 Comparative Genomics
Another approach to try and define the genome of LUCA is
based on the comparison of the gene content of extant
genomes to identify those genes inherited from the last
common ancestor that were retained in all cells during the
course of evolution. The first implementation of this
approach dates back to 1996 with the search for orthologous
genes* conserved in both pathogenic bacteria Mycoplasma
4 For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
81
The study of the smallest extant prokaryotic genomes has led
to a few estimates of the minimum number of genes that the
genome of a cellular organism may contain and could therefore have been present in the genome of LUCA.
One of the smallest cellular genome known as of today is
that of the endosymbiotic bacterium Carsonella ruddii
(Nakabachi et al. 2006). This is a gammaproteobacterium
that infects all species of psyllid, Hemiptera insects feeding
exclusively on plant sap. Its genome consists of 160
kilobases and contains 182 protein-coding genes. This
genome is also extreme in its base composition: 84 % of A
or T and only 16 % of C or G. Carsonella ruddii depends
very closely on its host since it is completely devoid of genes
involved in the biosynthesis of the membrane and in the
metabolism of lipids and nucleotides. In contrast, the
genome of this symbiont contains a large number of genes
encoding proteins involved in the synthesis of essential
amino acids (~18 % of genes). This symbiont is essential
to the survival of the host insect, which does not find these
amino acids in its single food source. Some authors interpret
this genomic reduction as a process comparable to that
experienced by mitochondrial and chloroplastic genomes.
Others, on the contrary, think that this is an evolutionary
dead end that will ultimately lead to the demise of this
symbiont. More recently, even smaller genomes have been
discovered such as the betaproteobacterium ‘Candidatus
Tremblaya princeps’ (139 kilobases, 121 protein-coding
genes) or the alphaproteobacterium ‘Candidatus Hodgkinia
cicadicola’ (148 kilobases, 169 protein-coding genes)
(McCutcheon and Moran 2012).
In general terms, the smallest sequenced prokaryotic
genomes contain a few hundreds of genes. They come
from symbionts or parasites whose highly specialised ways
of life have led to very intense genome reduction:
Nanoarchaeum equitans in Archaea and Mycoplasma and
Buchnera in Bacteria. The small genome size of these extant
cellular organisms is believed to be the result of recent and
independent genomic reduction events rather than a feature
inherited from a common ancestor.
4.1.5.2 Experimental Approaches
Systematic experiments of in vitro gene inactivation were
used to identify genes essential for maintaining cellular life.
The underlying assumption is that these essential genes
could be inherited from LUCA. The results show that not
all genes of a prokaryotic genome are necessary for the
survival of a cell. For example, of the 480 genes in the
genome of Mycoplasma genitalium, only two-thirds are
actually needed for growth in laboratory. Similarly, in Bacillus subtilis, only 271 of the 4,100 genes present in the
genome have proven essential to the maintenance of cellular
life in the laboratory. In the yeast Saccharomyces cerevisiae,
nearly 1,000 genes are detected as required. Despite significant variation according to the organisms studied and the
experimental methods used to determine the number of
essential genes, a ‘minimal’ cell seems to emerge from
these studies: it is a simple prokaryotic cell consisting of a
compartment defined by a membrane and performing typical
cellular functions:
1. Replication
2. Isolation of the compartment from the outer medium
3. Protein synthesis
4. A rudimentary metabolism for energy production
(glycolysis)
A major limitation of these experiments is that they
involve the inactivation of a single gene at a time. Thus,
the effect of the simultaneous inactivation of several individually dispensable genes is not taken into account (e.g.
two genes can be individually dispensable without being so
simultaneously). For example, the bacterium Escherichia
coli has genes coding for two types of ribonucleoside
diphosphate reductases that catalyse the reduction of ribonucleoside diphosphates into deoxyribonucleoside diphosphates under aerobic conditions and anaerobic conditions,
respectively. Inactivation of the genes encoding the enzyme
operating under aerobic conditions does not prevent the
growth of E. coli under anaerobic conditions. They are
therefore dispensable genes. Similarly, inactivation of
genes encoding the enzyme operating anaerobically does
not prevent the aerobic growth of E. coli. They are therefore
also dispensable genes. However, the simultaneous inactivation of genes encoding the two types of enzymes is lethal.
Finally, we must not forget that these experiments were
conducted in laboratory conditions that are optimal for the
microorganisms studied. The experimenters supplement all
their nutritional requirements; they are neither subjected to
stress nor are they in competition with other microorganisms. While most individual gene inactivation does
not prevent strain growth in the laboratory, microorganisms
that carry one such inactivation, however, are unable to
thrive in a natural environment where the number of essential genes is much more important.
4.1.5.3 Comparative Genomics
Another approach to try and define the genome of LUCA is
based on the comparison of the gene content of extant
genomes to identify those genes inherited from the last
common ancestor that were retained in all cells during the
course of evolution. The first implementation of this
approach dates back to 1996 with the search for orthologous
genes* conserved in both pathogenic bacteria Mycoplasma
4 For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
81