Computational tools and Interoperability in Comparative ... - CBS

Genome Comparisons
Figure 2.8: Deamination of cytosine (C) into uracil (U)
2.3.5 Base composition and DNA repair
Klebsiella is often found in plant products, root surfaces and living trees, fresh vegetables,
and foods with high content of sugars and acids, such as frozen orange juice concentrate.
Klebsiella pneumoniae can causes urinary tract infections and the NTUH-K2044 strain
was isolated from a patient with liver abscess and meningitis. The broad range of ecological
niches in which Klebsiella lives share the property of being rich in energy and nitrogen.
Nitrogen-fixing aerobic bacteria are known to have higher chromosomal GC content (McEwan
et al., 1998), explained by the nitrogen requirement to replicate the chromosome; an
AT base pairs contains 7 nitrogen atoms whereas a GC pair contains 8 nitrogen atoms.
Cytosine pairs are prone to mutation caused by spontaneous deamination into uracil
(Visnes et al., 2009) (figure 2.8). In E. coli the two enzymes uracil N -glycosylase and
apurinic (AP) endonuclease are responsible for the repair of this mutation. However, in
Buchnera aphidicola Cc, which is a small reduced genome, these two enzymes are absent
(confirmed by protein BLAST). A negative selection is likely to occur in organisms with
high chromosomal GC content and the lack of a functional repair mechanism. Hence, base
composition of the bacterial genome is by no means random and adjusting the overall GC
contant through evolution may be yet another way to adapt to the environment.
2.3.6 BLASTmatrix - proteome comparison
The BLASTmatrix tool allows for visualization of proteome similarity between larger
numbers of organisms. For each of the pairwise combinations of proteomes, a BLAST
is performed. Two proteins are declared homologous when 50% of the protein is aligned
and 50% of the residues within the alignment are conserved. For a report of proteome
A against proteome B, all homologous proteins are then grouped into families and the
similarity between A and B is calculated as the number of families having both organism
A and B represented. The BLAST report is cached, based on MD5 checksums of the
proteomes. This enables the tool to efficiently reuse previous results, when organisms
are added to a comparison. This is repeated for all N j=1 j combinations and for each
combination a square is drawn containing the following information: the similarity as
percentage of all families of A and B, the number of shared families and the total number
of families. A small example matrix is shown in figure 2.9. The percentage is used to
color-code the square to allow for easier overview of larger comparisons.
The software requires a configuration in XML as first argument. In appendix D.4
a Perl script is provided which automatically constructs a configuration that compares
all published Campylobacter proteomes, by querying the Genome Atlas Database. The
output of the BLASTmatrix configuration is shown in figure 2.10.
The software has been used in different publications (Binnewies et al., 2005, 2006) and
has been updated a number of times since. The older versions contained both BLAST
directions and showed the number of shared proteins, leaving the diagram redundant. The
recent version avoids this by instead plotting the shared families which renders the plot
symmetrical across the diagonal. This allows the lower triangle to be removed.
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