What's Nocardia. Nocardia species are
Gram-positive bacteria which grow in soils as well as animal
tissues. They can cause a disease in humans, nocardiosis. Since
treatment for nocardiosis heavily relies on chemotherapy, their
intrinsic multiple drug resistance is a serious problem. On the other
hand, some species of
Nocardia are known to produce antibiotics
and aromatic compound-degrading or converting enzymes. Recently,
Nemoto
et al. discovered an antibiotic, asterobactin, from a
clinical isolate. To elucidate the molecular basis of the versatility
of this organism, we determined the nucleotide sequence of the genome
of a clinical isolate
Nocardia farcinica IFM 10152 by
whole-genome shotgun strategy.
Why farcinica. Taxonomy of
Nocardiae is
complicated, especially in "
asteroides-complex". Many strains
of
Nocardia have been moved to different genera or species so
far. However, the species
N. farcinica
was found to be nearly homogeneous (
Laurent
et al.,
figure). In addition to this,
recently,
N. farcinica is the most frequently isolated species
in Japan.
How determined. We constructed small- (2 kb) and large-insert
(10 kb) genomic libraries, and generated about 115,000 sequences
(giving 9.5-fold coverage) from both ends of the genomic clones. The
sequence data were assembled by using
PHRED/PHRAP/CONSED package and
in-house scripts. Sequence gaps were closed by
transcriptional sequencing and primer walking. The final gap was
closed on 2 Sep., 2003 (my birthday:-). Genes were annotated by using
GLIMMER,
BLASTP,
FramePlot,
tRNASCAN-SE
and in-house scripts.
