Article

Working from the particular to the general--the development of comparative genomics--a meeting report from the 4th Annual Conference on Microbial Genomes.

Molecular Infectious Diseases Group, Institute of Molecular Medicine, University of Oxford, Headington, OX3 9DS, United Kingdom.
Molecular Microbiology (Impact Factor: 4.42). 07/2000; 36(5):1034-6. DOI: 10.1046/j.1365-2958.2000.01929.x
Source: PubMed

Full-text

Available from: Nigel J Saunders, Apr 20, 2015
Molecular Microbiology (2000) 36(5), 1034±1036
Working from the particular to the general ±
the development of comparative genomics ±
A meeting report from the 4th Annual Conference
on Microbial Genomes
Nigel J. Saunders
Molecular Infectious Diseases Group, Institute of
Molecular Medicine, University of Oxford, Headington,
Oxford, OX3 9DS, UK.
Each genome sequenced contains a wealth of information
on that particular strain. However, one of the central
challenges of the post-genome era is to use the information
from the sequenced example strains to investigate the
bacterial population and the species as a whole. Devel-
opments in this field were prominent at the latest TIGR
Microbial Genomes conference held in Chantilly, VA.
Comparisons are now becoming possible within clonal
populations over time, and between unrelated strains and
species
Pairs of genomes from a single species are now
available for Helicobacter pylori, Mycobacterium tubercu-
losis, Neisseria meningitidis and soon Escherichia coli.
The published comparison of the H. pylori genome
sequences (Alm et al., 1999) showed many differences
including reorganizations, polymorphisms in hypermu-
table loci and 6±7% differences in gene complement. R.
Fleischman (TIGR) presented the results of a compara-
tive analysis of the two sequenced M. tuberculosis
genome strains, H37Rv and CDC1551, which showed a
very different pattern of differences between two strains of
the same species namely, little evidence of genome
reorganization and very similar gene complements and
sequences. CDC1551 has a moderately larger chromo-
somal size due to the presence of 15 or 16 IS6110 as
opposed to the four copies present in H37Rv. The two
sequences have been compared using suffix trees and
this has identified a number of tandem repeats, insertions
and deletions which distinguish the two strains. Some of
the tandem repeats are associated with the surface
located putative virulence determinants, PPE±PGRS
proteins, the others are associated with proteins of
unknown function. Insertion±deletion events include
whole genes, one example being a region close to the
phospholipase C gene, where interestingly the genes that
are absent from H37Rv are present in both CDC1551 and
the unpublished Mycobacterium leprae sequence from
the Sanger Centre. One intriguing observation is that
when the presence of insertions and deletions is
investigated in multiple strains there appears to be a
relationship between the number of insertion and dele-
tions and the number of IS6110 copies that are present.
Whilst there is no evidence of a physical relationship
between the IS elements and the sites of the changes this
suggests that there may be an association between these
two processes of strain diversification.
F. Blattner (Univerity of Wisconsin) presented ongoing
work comparing the sequences of E. coli strains. His
group have identified in the region of 0.5 Mb of DNA that
is present in E. coli strain K-12 but is absent from the
sequenced strain of O157, and 1.3 Mb of sequence that is
present in O157 but absent from K-12. Rather than being
exclusively associated with a small number of large
regions they have identified 235 points scattered over
the whole chromosomal map at which these insertions or
substitutions can be identified. The smallest is an insertion
of 6 amino acids in a leader sequence. More classical
pathogenicity islands have also been detected and there
is an example in which the two strains have different
pathogenicity islands located at the same sequence
location adjacent to the leuX tRNA gene. Blattner's
group have made substantial progress in using these
polymorphic sites in order to investigate the wider E. coli
population using PCR primers to the flanking regions of
each. The differences at these sites cluster into clearly
definable groups which has the potential to form the basis
of a subdivision of strains into biologically similar groups.
This has revealed, amongst other things, that there are
naturally occurring strains that are very similar to K-12,
suggesting that this strain may indeed be representative
of some naturally occurring isolates despite its long
history of laboratory culture.
B. Tummler (Klinisce Forschergruppe) presented com-
parative analyses of Pseudomonas aeruginosa strains
which are characterized by rapid strain adaptation to new
Q 2000 Blackwell Science Ltd
Received 9 March, 2000; accepted 17 March, 2000. *For
correspondence. E-mail saunders@molbiol.ox.ac.uk; Tel. (144)
1865 222 347; Fax (144) 1865 222 626.
Page 1
environmental niches and in cystic fibrosis are associated
with a predictable series of changes affecting virulence
that occur regardless of the initial colonizing clone.
Comparison of strains considered to be part of a single
clone were considered to display differences of up to 10%
of their genomes. Detailed comparison of two members of
one circulating clone revealed hot spots for insertions and
an example of a hypervariable region with abnormal
%G1C composition and codon usage in which 80% of the
open reading frames (ORFs) were of unknown function
but in which the ORF density was the same as the rest of
the chromosome. The time frame for these changes is
thought to be short and the origin of some is recognizable
(for example one region was previously found in
Pseudomonas putida). The sites of insertion were
associated not only with tRNA genes but also sequences
capable of forming Holliday junctions. In contrast to these
large numbers of changes between isolates, when early
and late colonizing isolates from cystic fibrosis cases were
compared using signature tagged mutageneis to find the
changes responsible for the familiar changes in pheno-
type, it was shown that gain of only a very small number of
genes were responsible.
Comparative analyses are also possible at the level of
protein families. L. A. McCue (NY State Department of
Health) presented just such a comparison in which the
superfamiy of cAMP binding proteins were investigated in
the completed genome sequences using the
PROBE soft-
ware. This revealed that M. tuberculosis differs from the
other sequenced genomes in having a very large number
of apparently cAMP regulated proteins which include
cytoplasmic, internal membrane, and receptor-type pro-
teins and was the only bacterial species to date to have
translocases and esterases in this class of regulated
proteins. This type of analysis shows how major differ-
ences in metabolism can be rapidly detected using
genome sequences.
The theme of pursuing metabolic function through
comparative analysis was continued by S. G. E. Anderson
(Uppsala University) who has been comparing the
genomes of intracellular parasites, endosymbionts and
mitochondria. These studies reveal that these species
continue to loose genes and are in a continuous process
of becoming progressively more dependent upon the
metabolisms of the cells in which they reside. Whilst they
are loosing genes through degeneration there is little
evidence of gene acquisition from other sources, probably
due to their relative isolation within the cells that they live.
Their most striking observation comes from a comparison
of the mitochondrial genes that are located in the
chromosome and mitochondrial chromosomes in yeast.
Investigation of the approximately 400 genes encoding
mitochondrial functions and considering those that have
homology to bacterial genes it seems likely that the
original bacterial symbiont did not provide genes for ATP
production, and perhaps could not produce ATP. This led
to the suggestion that the acquisition of the endosymbiont
ancestor of mitochondria was related to the control of
toxic intracellular oxygen at a period in evolutionary
history when oxygen concentrations were increasing
and that only later did the mitochondrial ATP translocases
evolve. The corresponding genes in the chromosome
then developing in the chromosome de novo rather than
by translocation from the ancestor symbiotic bacterium.
These comparative approaches have revealed many
differences between strains, but also reveal significant
qualitative differences in the evolutionary biology and the
processes of change in each of the different species
groups that have been investigated. Horizontal transfer is
clearly widespread, indeed W. F. Doolittle (Canadian
Institute for Advanced Research) suggests that it is
sufficient to undermine our current models of phylogeni-
tics and evolutionary trees. However, the comparative
analysis of microbial genomes reveals important differ-
ences in the extent, rate and characteristics of horizontal
exchange, and other processes generating change within
and between different bacterial species.
The use of arrays, generated using genome sequence
data, has added a further dimension to comparative
analyses: comparisons of the same strain over time. In
the first example, M. Laub (Stanford University) presented
the use of arrays to study the life cycle of Caulobacter
crescentus. This approach has great promise for use in
other systems in which there are clearly separated phases
of the cell cycle. They have been able to clearly
demonstrate the expression of the genes associated
with flagellar biosynthesis in the order in which they are
assembled. They have also made many new observations
including the identification of over 400 new cell cycle
regulated genes and 13 operons that are under the control
of CtrA. The second example, is a study of yeast evolution
in chemostat cultures. F. Rosenzweig (University of
Florida) discussed their array based analysis which
demonstrated that there was a very rapid change in the
pattern of mRNA production following strong selection
(glucose limitation) and that there is a very rapid
reorganization of the cellular metabolism and duplication
of some genes that are adaptive to the changing
environment. This emphasises the enormous flexibility
that cellular systems have, presumably following only
minor changes in the genome that can have a profound
effect upon cell function.
This comparative approach, although perhaps still in its
infancy, is already providing new and important insights
into cell biology, adaptation, evolution, and differences
within and between strains. As the number of genomes
that are available continues to grow, the power of
comparative genomics is clearly becoming an increasingly
Meeting Report 1035
Q 2000 Blackwell Science Ltd, Molecular Microbiology, 36, 1034±1036
Page 2
important and pervasive field affecting many areas of
microbial research and may ultimately become the prime
reason for sequencing additional genomes.
Acknowledgement
N.J.S. is supported by a Wellcome Trust Fellowship in
Medical Microbiology.
References
Alm, R.A., Ling, L.-S., Moir, D.T., King, B.L., Brown, E.D.,
Doig, P.C., et al. (1999) Genomic-sequences comparison
of two unrelated isolates of the human gastric pathogen
Helicobacter pylori. Nature 397: 176±180.
1036 Meeting Report
Q 2000 Blackwell Science Ltd, Molecular Microbiology, 36, 1034±1036
Page 3