Biology Reference
In-Depth Information
Fatty acid metabolism
Blosynthesis cofactors
Rickettsia
Buchnera
Wigglesworthia
Cell structure
Cell processes
Tr ansport
Nucleic acids
Tr anslation/protein fate
Tr anscription
Energy metabolism
Regulatory functions
DNA metabolism
Central intermediary
metabolism
Amino-acid blosynthesis
0 20 40 60 80 100 120 140 160
Number of genes in each category
FIGURE 4.3
Comparative analysis of the number of genes present in each functional category described in
the genomes of
Wigglesworthia
,
Buchnera
, and
Rickettsia
. * denotes the categories, biosynthesis of cofactors
in
Wigglesworthia
genome, and amino acid biosynthesis in
Buchnera
genome that contain higher numbers of
genes in comparison to the other two symbiont genomes analyzed.
represents about 85% of the genome (Akman et al., 2001), assuming an average size of 1 kb per
gene (Shigenobu et al., 2000). The
E. coli
array contains 4290 ORFs corresponding to its
sequenced genome, and functional roles have been assigned to 1938 of these ORFs. Of the 1800
heterologous genes detected from
Sodalis
, 1158 had functional roles assigned in
E. coli,
while
the remaining 642 ORFs detected corresponded to genes with hypothetical functions. Although
the
Sodalis
genome is about half the size of that of
E. coli
, comparative analysis revealed that
it contained a high proportion of the genes necessary for all of the amino acid biosynthetic
pathways, regulatory functions, translation, and transcription and for nucleic acid biosynthesis.
Many genes involved in the biosynthesis of cofactors, replication, and transport functions were
also found to be present, and most of the DNA repair and recombinase orthologs of
E. coli
involved in direct damage reversal, base-excision repair, mismatch repair, recombinase pathways,
and nucleotide-excision repair were retained. Genes involved in carbon-compound catabolism,
central intermediary metabolism, fatty acid phospholipid metabolism, cell processes, and cell
structure, however, were fewer in number in comparison to the
E. coli
genome. Based on array-
hybridization analysis,
Sodalis
appears to have respiratory oxidases, NADH dehydrogenase
complex enzymes, and a complete TCA cycle. It can grow on several sugars including galactose,
fructose, and rafÝnose, as well as the amino sugars
N
-acetyl-
D
-glucosamine, the methylpentoses
L
-fucose,
L
-rhamnose,
L
-arabinose, and xylose. In fact,
in vitro
carbon-substrate-assimilation tests
suggest that
Sodalis
may be utilizing primarily
N
-acetylglucosamine and rafÝnose as its primary
carbon sources
in vitro
(Dale and Maudlin, 1999). Apparently
Sodalis
has many of the capabilities
of free-living bacteria, which is supported by
in vitro
cell-free culture for this organism (Welburn
et al., 1987; Beard et al., 1993). While the array-hybridization approach has provided us with a
general understanding of the genomic coding capacity of
Sodalis
, it lacks information on loci
not represented in the
E. coli
genome. There are at least two such examples; the Ýrst is a
chitinase
characterized from
Sodalis
that is absent in the
E. coli
genome (Welburn et al., 1993), and the
second is the pathogenicity island genes that may help
Sodalis
invade the tsetse cells via a Type
III secretion system (Dale et al., 2001). Thus, the array analysis has provided a broad under-
standing of the general aspects of the
Sodalis
genome functions.