Biology Reference
In-Depth Information
noncoding intergenic regions account for the difference between the two genomes
(Table 3.1).
One
of the most signiÝcant Ýndings obtained from the
Buchnera
(Sg) genome sequence and its subse-
quent comparison to the
(Ap) genome is the fact that the two genomes show perfect
synteny with no detected inversions, translocations, or duplications, despite 50 to 70 million years
of independent evolution. There are also no indications of genes horizontally transferred into these
genomes subsequent to their divergence (Tamas et al., 2002).
Unlike the remarkable stability observed in gene content and gene order, nucleotide substi-
tutions at synonymous sites (Ks) are surprisingly high, close to saturation (Tamas et al., 2002).
Since little variation is observed among genes, these rates are expected to reÞect the intrinsic
mutation rate. Based on the assigned dates for divergences of strains of
Buchnera
, it has been
possible to estimate substitution rates among lineages. The genomic substitution rate has been
estimated at 9.0
Buchnera
10
synonymous and 1.6
10
nonsynonymous substitutions per site per
Ï9
Ï9
year for chromosomal genes in
Buchnera
(Sg) and
Buchnera
(Ap), averaged over all genes
(Tamas et al., 2002).
The genomic stasis observed in
Buchnera
can most likely be attributed to its speciÝc ecological
niche. Locked in their intracellular environment with few or no possibilities to take up external
DNA or a need for doing so, these genomes have remained remarkably conserved. In a global
comparison of the relative frequency of rearrangements and insertions/deletions compared to nucle-
otide substitutions,
Buchnera
were found to represent the least variable genomes, whereas
E. coli
and
Salmonella
were found to have the most variable genomes among all the analyzed genome
pairs (Tamas et al., 2002).
This extreme stasis may be related to the fact that the
Buchnera
genomes are the only bacterial
genomes known so far in which a
recA
gene is not present (Tamas et al., 2002). The product of this
gene, recombinase A, catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the
ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization
of homologous single-stranded DNAs (Dale, 1998; Belotserkovski and Zarling, 2002). The loss of
this gene is expected to lower the incidence of recombination events, although it cannot be excluded
that
recA
-independent recombination pathways are present and may partially compensate for this loss.
The
recF
gene involved in DNA replication and normal SOS induction has also been eliminated
in these genomes. In
Buchnera
(Sg), additional genes involved in base-excision repair, such as
endA
,
lig
,
ung
,
mfd,
and
phrB
, have started to accumulate mutations. In addition to impaired
capabilities for DNA recombination, this is expected to inÞuence the process of DNA repair in
Buchnera
(Sg). The presence of as many as 120 genomic copies per
Buchnera
cell (Komaki and
Ishikawa, 1999) may be a creative way of compensating for the loss of
recA
and DNA-repair-
associated genes: once severe damage to the active genomic copy occurs, another copy takes on
the leading role.
DETERIORATION OF THE
BUCHNERA
GENOMES
The
Buchnera
genomes are two of the most highly reduced genomes described to date. A compar-
ison of the two genomes conÝrms that they are still in the process of erasing gene sequences, albeit
at a low rate. Detailed analyses of pseudogenes and intergenic DNA have provided clues about the
patterns and processes of genome deterioration. Interestingly, the genes targeted by mutations are
not a random subset of the
Buchnera
genomes; almost half of the identiÝed pseudogenes (18 out
of 38) in
Buchnera
(Sg) belong to the three blocks of genes coding for functionally related proteins
C
YSTEINE
B
IOSYNTHETIC
G
ENES
A total of 6 of the 46 genes in
Buchnera
(Sg) that are related to amino-acid biosynthesis appear
to be mutationally inactivated and are all involved in cysteine biosynthesis (
cysDGHINQ
). The
