Biology Reference
In-Depth Information
G
ENOME
D
EGRADATION
: A G
RADUAL
P
ROCESS
Currently, there are two different models that attempt to explain the extensive genome reduction
observed in
Buchnera
. On the one hand, it has been suggested that genome reduction has resulted
from the removal of large pieces of DNA mediated by repeated sequences (Moran and Mira, 2001;
Tamas et al., 2002). On the other hand, genome reduction has also been explained by the gradual
accumulation of deletions of small sizes (Silva et al., 2001). As we will argue below, these scenarios
are not mutually exclusive.
Thus, it seems likely that the process of genome reduction was initially obtained by large
deletion events leading to a relatively rapid disappearance of large fragments of DNA. We can call
this stage phase I; it is characterized by the early stages of the integrative process, soon after
acquisition of the obligate host-associated lifestyle. Unfortunately, it is difÝcult to conÝrm that
large fragments of DNA were once eliminated from the ancestral genome because these processes
happened hundreds of millions of years ago and left few traces in modern
Buchnera
genomes.
However, the rate of sequence evolution during the past 50 million years is too low to account for
the extensive sequence loss that has occurred since the divergence of
Buchnera
from its free-living
relatives, providing indirect support for large, repeat-mediated deletions at an earlier stage.
Once recombination frequencies at repeated sites were reduced due to the loss of repeated
sequences and recombination genes, deletions involving single to several nucleotides started to
dominate the reductive processes. We can call this stage phase II; the rate of gene removal witnessed
today (14 genes/50 million years per two genomes) (Tamas et al., 2002) is an example of the slow
rate at which sequences are lost during this second phase.
Several examples of weakly as well as heavily mutated genes have been identiÝed in
B.
aphidicola
(Sg). In addition to genes like the
cysNDHGIQ
,
murCEF
, and
ddlB
homologs, which
are only weakly affected by mutations, we have identiÝed noncoding DNA that shows little or no
similarity with orthologs in the other genome (
cmk
,
ycfM, asnA
,
bioH
,
folE
) (Tamas et al., 2002).
In some cases, an existing functional gene has been identiÝed in one genome, whereas there is a
long spacer at the same position in the other genome showing no sequence similarity to the identiÝed
gene. This may be explained by an early inactivation followed by a rapid rate of nucleotide
substitutions, eroding all traces of the ancestral gene. Examples of such extreme cases are
cspC,
hns,
and
ycfM,
which display no deducible sequence similarity to the corresponding locus in the
other genome (Tamas et al., 2002). Thus, gene elimination in
Buchnera
has been shown to occur
in a slow step-by-step manner, also observed in other obligate host-associated genomes such as the
Rickettsia
genomes (Andersson et al., 1998; Andersson and Andersson, 1999a,b, 2001).
Genes in
Buchnera
tend to be slightly shorter than their orthologs in
E. coli
(Charles et al.,
1999). The reduction of gene length is mainly seen at the 3 ends of
Buchnera
, which may be
due to a higher frequency of termination codons in A+T-rich genomes (Oliver and Marin, 1996).
Perhaps the most drastic example of gene shortening described so far is found in the psyllid
endosymbiont
Carsonella ruddii,
yet another example of parallel evolution of a prokaryote and
its host (Clark et al., 2001)
. C. rudii
proteins appear to be on average 9% shorter than their
E.
coli
homologs. The reduction of intergenic regions is in some cases so extreme that it results in
operon fusions. In addition, they have extremely low G+C content values, sometimes as low as
10%. These genomic features suggest that this could be one of the most highly derived endo-
symbiont genomes identiÝed so far.
Despite the conservation of the gene order in
Buchnera
(Sg)Ï
Buchnera
(Ap) (Tamas et al.,
2002) and genome size in
Buchnera
of
R. padi
and
Melaphis rhois
(Wernegreen et al., 2000), a
further reduction of
Buchnera
genomes down to 450 kb has been observed (Gil et al., 2002).
These, supposedly the smallest bacterial genomes, have been identiÝed in
Buchnera
present in
Lachninae, a subfamily distant to Aphidinae and considered the most ancestral group within the
Aphidoidea (Martinez-Torres et al., 2001). These genomes may contain as few as 396 protein-
coding genes. The variation in genome size of the primary aphid endosymbionts may be attributed
