Conclusions from Genome Comparisons:
Wolinella succinogenes vs. its Close
Relatives Helicobacter pylori and Campylobacter jejuni.
Sequencing & Assembly
The genome of Wolinella was sequenced
by a whole genome shotgun approach, using 2 plasmid libraries and the end-sequences
of a Fosmid library. Assembly and gap closure was conducted using the Phred/Phrap/Consed
package (University of Washington) and the software ControlCenter
and EndSeqMapper
(Max-Planck-Institute for Developmental Biology). Annotation was done using
the software GENDB
developed by the University of Bielefeld, Germany.
Analysis & Annotation
After completion of the genome sequencing
annotated ORFs were analysed for their role in the physiology and assigned
COG
categories (Tatusov et al., 1997). Motifs known to be critical for
ori,
genes present close to the ori, and GC
skew analysis (Grigoriev et al.,
1998) were used to narrow down the location of the ori. GeneWiz
(Pedersen et al., 2000) was used to visualise the all the features.
Genome Comparison
We performed whole genome alignments using
MUMmer
(Delcher, et al., 1999) and Open Reading Frames (ORFs) comparisons
to look for similarities at the protein level using BlastX
(Altschul,
et
al., 1997).
The W.succinogenes genome (chromosome)
was compared against Campylobacter jejuni (Parkhill, et al.,
2000) and two Helicobacter pylori strains 26695 (Tomb, et al.,
1997) and J99 (Alm, et al., 1999). As a control C.jejuni
against H.pylori 26695 and J99 and also H.pylori 26695 against
J99 were performed. 1883 of the W.succinogenes ORFs were used for
the Blast search
MUMmer
MUMmer
assumes that the sequences are closely related and looks for Maximum Unique
Matches (MUMs) in both the genomes. The colinearity is apparent in case
of the two H.pylori strains comparisons but not so in other cases.
BlastX
The Blast
comparisons clearly show that a vast majority of proteins (873) are present
in all the three species compared, but not necessarily in the same order.
We also find that Wolinella shares more genes with Campylobacter.
Symbiont, Commensal or Pathogen ?
W. succinogenes was originally isolated
from the bovine rumen and until now not been considered to be pathogenic.
Its close relative H. pylori in contrast is a human pathogen that
causes peptic ulcer and gastric cancer. Since both species are also related
to the pathogen Campylobacteraceae, we have compared the genomes of the
two H. pylori strains J99 and 26695 to Wolinella succinogenes,
and the one of Campylobacter jejuni.
Interestingly, the gene inventory of Wolinella
turned out to contain a large number of virulence homologs that question
its perception as a non-pathogenic organism.
Virulence Factor Homologs
Many factors that contribute to the virulence
of H. pylori can be found in the genome of W. succinogenes.
For example genes necessary for adhesion, invasion and persistence in the
host organism. Further W. succinogenes contains a 28 kb region,
flanked by transposases, which is characterized by an increased AT content,
coding for typical virulence genes, e.g. members of the type IV
secretory pathway and cytotoxins. This region fulfills all criteria of
a pathogenicity associated island (PAI).
|
|
Wsu
DSM 1740
|
Hpy
J99
|
|
urease
|
-
|
+
|
|
pathogenicity
island
|
+
|
+
|
|
hemolysin
A
|
+
|
+
|
|
adhesion
|
+
|
+
|
|
pilin
|
+
|
+
|
|
invasins
|
+
|
+
|
|
flagellum
|
+
|
+
|
|
flagellin
|
+
|
+
|
|
antigenicity
|
+
|
+
|
|
neutrophil
activation NAP
|
+
|
+
|
|
resistance
|
+
|
+
|
|
toxins
|
+
|
+
|
|
type
IV secretion (vir)
|
+
|
+
|
|
superoxide
dismutase
|
+
|
+
|
|
protease
pspA
|
+
|
+
|
Covacci,
et
al. 1999; Hacker & Kaper 2000
Conclusions
-
W. succinogenes, H. pylori and
C.
jejuni show no genome wide colinearity.
-
Local colinearity exists and the gene content
is similar in all three species.
-
W. succinogenes contains a large inventory
of virulence factors
-
Using genome comparisons it should be possible
to define sets of genes that are responsible for host specificity. For
example H.pylori genes involved in human infection.
-
Contradicting analysis based on 16S RNA, W.
succinogenes should not be considered a member of the Helicobacteraceae
but rather viewed as an independent group.
References
-
Alm, R.A. et al. Genomic-sequence Comparison
of Two Unrelated Isolates of the Human Gastric Pathogen Helicobacter
pylori. Nature 397:176-180(1999).
-
Altschul, S.F. et al. Gapped BLAST
and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic
Acids Res. 25:3389-3402 (1997).
-
Covacci, A. et al. Helicobacter
pylori Virulence and Genetic Geography. Science 284:1328-1333 (1999).
-
Delcher, A.L. et al. Alignment of whole
genomes. Nucleic Acids Res. 27:2369-2376 (1999).
-
Ewing, B. et al. Base-calling of automated
sequencer traces using phred. I. Accuracy assessment. Genome research 8:175-185
(1998).
-
Ewing, B. et al. Base-calling of automated
sequencer traces using phred. II. Error probabilities. Genome research
8:186-194 (1998).
-
Fleischmann, R.D. et al. Whole-Genome
Random Sequencing and Assembly of Haemophilus influenzae Rd. Science
269:496-512 (1995).
-
Hacker, J. et al. Pathogenicity Islands
and the Evolution of Microbes. Annu. Rev. Microbiol. 54: 641-679 (2000).
-
Grigoriev A. Analyzing genomes with cumulativeskew
diagrams. Nucleic Acids Res. 26:2286-2290 (1998).
-
Meyer, F. et al. GenDB annotation package.
Bioinformatics Group Bielefeld, unpublished.
-
Parkhill, J. et al. The genome sequence
of the food-borne pathogen Campylobacter jejuni reveals hypervariable
sequences. Nature 403:665-668 (2000).
-
Pedersen A.G. et al. A DNA structural
atlas for Escherichia coli. J.Mol.Biol. 299: 907-930 (2000).
-
Simon, J. et al. The Genus Wolinella.
In: Dworkin et al., eds., The Prokaryotes, 3rd edition, New York,
Springer-Verlag (2000).
-
Tatusov, R.L. et al. A genomic perspective
on protein families. Science 278: 631-637 (1997)
-
Tomb, J-F. et al. The complete genome
sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547
(1997).
Last
update: 27.06.2003
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