Last modified: Tue Jul 1 15:13:27 JST 2014

One of our goals is ASAP (Activation of Silent Antibiotic Productivity),
an approach to finding novel antibiotics.

Jun Ishikawa*, Yasutaka Hoshino, Keiko Ishino, Haruyo Kurita,
Kazuhiro Chiba, Shoko Fujii and Kenta Shibuya
National Institute of Infectious Diseases
Masahira Hattori and Atsushi Yamashita Kitasato Institute for Life Sciences, Kitasato University
Yuzuru Mikami, Katsukiyo Yazawa and Kenjiro Takeda Medical Mycology Research Center, Chiba University

 News 
[2012-10-08] The Nocardia brasiliensis ATCC 700358 genome is browsable on the GView.
[2012-03-13] The Nocardia cyriacigeorgica GUH-2 genome is browsable on the GView.
[IMPORTANT] Nucleotide sequences of pNV vectors have been updated.

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Browse Genome (GView powered by Ajax)
Browse genome with graphical user interface, Search genes by keyword...
BLAST search
BLAST against the genomic sequence, CDSs...
Download data
Download the annotation table and FASTA-formatted genomic sequence, CDSs, RNAs ...
Distribution
Genomic DNA clone
An ordered plasmid library was constructed from the large-insert shotgun library (KNL) used in the genomic sequencing. Available clones are listed here. Please request plasmid DNA via e-mail (up to 10 plasmid DNAs at a time).
Nocardia-E. coli shuttle plasmid vector
Low and high copy-number vectors are available.
Bacterial strain
The strain IFM 10152 is available from Medical Mycology Research Center, Chiba University. Please contact Prof. Y. Mikami.
Microarray
Hmmm...
Publication
Ishikawa, J., et al. The complete genomic sequence of Nocardia farcinica IFM 10152. Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930 (2004) [PNAS] [PubMed] [PubMed Central]
Ishikawa, J., et al. Contribution of rpoB2 RNA polymerase β subunit gene to rifampin resistance in Nocardia species. Antimicrob. Agents Chemother. 50:1342-1346 (2006) [AAC] [PubMed] [PubMed Central]
Chiba, K., et al. Construction of a pair of practical Nocardia-Escherichia coli shuttle vectors. Jpn. J. Infect. Dis. 60:45-47 (2007) [JJID] [PubMed]
Hoshino, Y., et al. Monooxygenation of rifampicin catalyzed by the rox gene product of Nocardia farcinica: structure elucidation, gene identification and role in drug resistance. J. Antibiot. 63:23-28 (2010) [JA] [PubMed]
Hoshino, Y., et al. Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica. J. Bacteriol. 193:441-448 (2011) [JB] [PubMed]
Other papers are listed in here.
Data deposition
The genomic sequence has been deposited in the DDBJ database under accession numbers:
AP006618 (DDBJ|NCBI), AP006619 (DDBJ|NCBI) and AP006620 (DDBJ|NCBI)
Repeats
Analyzed by Tandem Repeats Finder (TRF):
Chromosome | pNF1 | pNF2
Analyzed by Inverted Repeats Finder (IRF):
Chromosome | pNF1 | pNF2
Selections of genes
Drug resistance genes (Resistome)
Virulence genes
Cytochrome P450 genes
Ribosomal protein genes
Ribosomal RNA genes
tRNA genes sorted by [position] [amino acid]
Experimentally confirmed genes
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.

Table. Current status of the genome


Chromosome pNF1 pNF2

Topology circular circular circular
Length (bp) 6,021,225 184,026 87,093
G+C content (%) 70.8 67.2 68.4
Copy number* 1 0.7 1.8
Protein-coding gene 5,697 165 93
rrn operon (16S-23S-5S) 3 0 0
tRNA gene 53 0 0

*The copy numbers of pNF1 and pNF2 were estimated from the statistical distribution of random reads between the plasmids and the chromosome.

Nomenclature and Style
In accordance with the international standards, we recommend the following style:
For genes: dnaA, nfa12340 (all italicised)
For proteins: DnaA, Nfa12340 (Roman and Initial Upper)
Gallery
Genome map images, photos, download ranking, gene ranking...:-)

Related links
Third party N. farcinica genome databases
CAZy (Carbonhydrate-Active enZymes) (AFMB)
CBS Genome Atlas
CUTG - codon usage
DBGET/KEGG (GenomeNet) - pathway -
DOLOP - lipoproteins -
Entrez Genomes (NCBI)
GIB (DDBJ)
GTOP (DDBJ) - protein structure -
MBGD (NIBB)
HAMAP (ExPASy) - proteome -
MEROPP - peptidase -
tigr cmr (TIGR)
Actinomycete Genomes
Mycobacterium tuberculosis ( Sanger | TubercuList | TIGR )
Causative agent of tuberculosis.
Mycobacterium smegmatis (TIGR)
Non-pathogenic mycobacteria.
Corynebacterium diphtheriae (Sanger)
Causative agent of diphtheria.
Streptomyces avermitilis (Kitasato Univ., NIID & NITE)
The industrial microorganism.
Streptomyces coelicolor A3(2) (Sanger | Streptomyces UK)
The most famous model strain of Streptomyces. Please remember that this strain taxonomically belongs to Streptomyces violaceoruber. Don't mistake S. coelicolor A3(2) (e.g. ATCC BAA-471) for S. coelicolor (Müller) (ATCC 23899)!!
Streptomyces griseus NBRC 13350 (Univ. Tokyo, Kitasato Univ. & NIID)
A streptomycin producer
Kitasatospora setae NBRC 14216 (Kitasato Univ., NITE, NIID, et al.)
A setamycin (bafilomycin B1) producer
Saccharopolyspora erythraea NRRL 2338 (Univ. Cambridge)
An erythromycin producer. circular chromosome.
Rhodococcus equi 103S (Sanger)
Causative agent of bronchopneumonia in horses. The complete sequence without annotation is available via FTP.
Rhodococcus jostii RHA1 (Genome Canada)
A PCB-degrader.
Kineococcus radiotolerans (JGI)
Belongs to Frankiae. Draft genome sequence with annotation is available.
Frankia sp. CcI3 (Univ. Connecticut & JGI)
A symbiotic nitrogen-fixing actinobacterium.
Frankia alni (Genoscope & CNRS)
A symbiotic nitrogen-fixing actinobacterium. Complete sequence is available here.
Genomes assembled by me:-)
Nocardia farcinica (6.02Mb)
This genome.
Streptomyces avermitilis (9.03Mb)
Proc. Natl. Acad. Sci. USA 98:12215-12220 (2001) [PubMed]
Nature Biotechnology 21:526-531 (2003) [PubMed]
Mycoplasma penetrans (1.36Mb)
Nucleic Acids Research 30:5293-5300 (2002) [PubMed]
Tools
FramePlot
CUPlot
is a derivative of FramePlot, and helps identification of protein-coding genes by using the codon usage of organisms you interested.
2ndFind
is a web-based support tool to find secondary metabolite biosynthetic gene cluster.
Miscellaneous
Nocardiosis (CDC)
Edmond Nocard (who discovered the first Nocardia)
The Society for Actinomycetes Japan (SAJ)
Actinomycetologica (the official newsletter of the SAJ)
The Journal of Antibiotics (the official journal of the SAJ)
Digital Atlas of Actinomycetes
Genomes OnLine Database (GOLD)
NCBI
Entrez Genome
Entrez Genome Project
nBlog
Dr. Masanori Okanishi, R.I.P. Dr. Masanori Okanishi, who is the founder of our lab, passed away on June 15th, 2013. He had developed the methods for preparing and regenerating streptomycete protoplasts (J. Gen. Microbiol. 80:389-400, 1974). It is certain that there was no progress in Streptomyces genetics without the methods. He was a really...»more
Latest Nocardia Papers in PubMed
[Cerebral nocardiosis as surprising cause of a convulsive seizure]. Kontturi A, Sonninen P, Soilu-Hnninen M, Talve L, Rahi M, Oksi J, Hohenthal U; Duodecim

*Correspondence to: Jun ISHIKAWA <jun(a)nih.go.jp>
Current address: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo
Any comments would be appreciated! Usage statistics