Rickettsia conorii complete genome sequencing: Preliminary survey
H. Ogata1, S. Audic1, P. Cossart2,
J. Weissenbach3, J. M. Claverie1, D. Raoult4
1Structural and Genetic Information, CNRS-UMR 1889, Marseille, FRANCE;
2Bacteria-Cell Interaction Unit, Institut Pasteur, Paris, FRANCE;
3Genoscope, Evry, FRANCE;
4Rickettsia Unit, CNRS-UPRESA 6020, Marseille, FRANCE
Purpose: Rickettsia conorii is the causative agent of Mediterranean
spotted fever, a severe disease transmitted by ticks. It is a
gram-negative bacterium that moves and multiplies within
eukaryotic host cell cytoplasm. The bacterium is closely related to
R. prowazekii which causes louse-borne typhus and whose complete genome
has been determined in 1998. Unlike R. prowazekii, R. conorii rapidly moves
inside the host cell cytoplasm by triggering actin polymerization. Comparative
genomic sequence analysis of R. conorii and R. prowazekii will shed light on
the adaptive gene-loosing process characteristic of intracellular parasites.
Methods and Materials: The whole genome sequence of R. conorii was
determined under contract with the Genoscope using bacterial DNA from
the Rickettsia Unit (UPRESA 6020, Marseille). Sequence analysis and
annotation were performed by the Structural & Genetic Information Laboratory
(UMR 1889, Marseille) and the Bacteria-Cell Interaction Unit (Institut Pasteur,
Paris) for the intracellular motility aspect.
Genes were identified using SELFID (Audic & Claverie, 1998) and a comparative
R. conorii/R. prowazekii database built in AceDB. Predicted ORFs were examined
for their similarity to known proteins and motif/domain
content. Metabolic pathways were constructed with the use of
KEGG (Ogata et al., 1999).
Results: At the time of this writing, sequencing of the R. conorii genome
(1.24 Mbp) is nearly completed. Estimated completion and coverage were 99%
and 8 fold, respectively. We identified 1,000 putative protein coding
genes. Among these, 60% had similarity to proteins of known function, 30%
had similarity to proteins of unknown function, and the rest (10%) were
orphan ORFs apparently specific to R. conorii. Most of amino acid synthetic
enzymes are absent.
In R. conorii, DNA sequences homologous to 9 pseudogenes from
R. prowazekii were identified. Of these nine, 2 are predicted
to code for intact proteins and 7 are to harbor pseudogenes.
The genome of R. conorii thus appears to be experiencing the genome
reduction phenomena already described for R. prowazekii. In addition, the
analysis of the R. conorii genome revealed original and surprising
structures that will be described in detail.
Conclusion: The complete genome analysis of R. conorii, and its comparison
to R. prowazekii will shed light on the evolutionary
mechanisms to adapt to intracellular parasitism and the characteristic
life-cycle of the tick-borne bacterium.
Genomes 2000
(Apr 11-15, 2000, Paris, France)