Kitasatospora setae NBRC 14216T
open/close allAbout this Microorganism
Courtesy of Prof. Takahashi (Kitasato Institute)
Bacteria within the genus Kitasatospora exhibit similar life style and morphology to Streptomyces species. Kitasatospora is also comparable to Streptomyces in its capacity to produce bioactive secondary metabolites. On the other hand, there are clear phenotypic criteria to distinguish Kitasatospora from Streptomyces such as the difference in cell wall composition; cell wall peptidoglycan of Streptomyces species contain the LL isomer of diaminopimelic acid (DAP), while K. setae contains both LL- and meso-DAP.
Kitasatospora setae NBRC 14216T (= KM-6054T) is a soil-habiting bacterium which is known to produce setamycin (bafilomycin B1) and bafilomycin A1, specific inhibitors of vacuolar ATPase and commonly used as biochemical reagents for investigation of molecular transport in eukaryotic cells.
The genome was composed of a single linear chromosome of 8,783,278 bp with 127,148 bp of terminal inverted repeats (TIRs). These characteristics in the genome topology were similar to those of Streptomyces. A total of 24 genes or gene clusters in the K. setae genome were predicted to be involved in the biosynthesis of secondary metabolites, underscoring the importance of the genus Kitasatospora as the source of bioactive compounds. Furthermore, molecular phylogenetic analysis and genome-wide comparison of genes related to morphological differentiation and cell wall biosynthesis provided further insights into the evolutional relationship of Streptomyces and Kitasatospora.
Project history
2010-11-11 ..... 1
Release of the Kitasatospora setae NBRC 14216T genomic sequence data | We published the genomic data of Kitasatospora setae NBRC 14216T (= KM-6054T). |
Summary of the genomic data
| Genomic size | 8,783,278 bp | ||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| G+C content | 74.20 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of ORFs assigned | 7,569 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Percentage of the coding regions | 87.60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Percentage of the intronic regions | 0.00 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of rRNA genes |
27
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| Number of tRNA genes |
74
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| Number of other features (misc_RNA,misc_feature,repeat) |
157
|
General Procedure
The nucleotide sequence of the K. setae NBRC 14216T genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE-DOB.
General Procedure
- DNA shotgun libraries
DNA shotgun libraries with inserts of 1.6 and 6.5 kb in pUC118 vector (TaKaRa) was constructed.
- Fosmid library
A Fosmid library with inserts of 37 kb in the pCC1FOS fosmid vector was constructed using the CopyControl Fosmid Library Production Kit (Epicentre).
- Nucleotide sequencing
Plasmid and fosmid clones were end-sequenced using dye-terminator chemistry on an ABI 3730xl DNA Analyzer (ABI) or Base Station DNA Fragment Analyzer BST-0100 (MJ Research, Inc.). Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled by PHRAP/CONSED softwere (http://www.phrap.org).
- Gap closing
Gaps between the assembled sequences were closed by sequencing PCR products which bridge two neighboring contigs.
- Validation of the assembled sequence data
Optical maps and sequence contigs were compared according to their restriction pattern. Finally, each base of K. setae NBRC 14216T genome was ensured to be sequenced from multiple clones and from both directions with Phrap quality score ≧ 70 or from one direction with Phrap quality score ≧ 40.
Gene identification and annotation
- Putative non-translated genes were identified using the Rfam, tRNAscan-SE and ARAGORN programs.
- For the prediction of protein-coding genes, GLIMMER3 programs were used. The initial set of ORFs was manually selected from the prediction result in combination with BLASTP and FramePlot.
- Similarity search results against Uniprot, Interpro and HAMAP database were used for functional prediction. The KEGG database was used for pathway reconstruction.
- Putative ORFs related to mobile genetic elements were oredicted and their boundaries were inderred with the assistance of GenomeMatcher software.
