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Sphingobium japonicum UT26S (= NBRC 101211)

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close this sectionAbout this Microorganism


Photo by Dr. Nagata in Tohoku University

-Hexachlorocyclohexane (-HCH) is a halogenated organic insecticide, which was once used widely throughout the world, but has been prohibited in many countries.
Use of -HCH causes serious environmental problems because of its toxicity and long persistence in upland soil. Sphingobium japonicum UT26S utilizes -HCH as the sole source of carbon and energy under aerobic conditions. Fifteen lin genes involved in -HCH degradation has been identified.

Sphingomonas-related strains are well known to degrade wide range of natural and xenobiotic compounds, such as chlorinated phenols, polychlorinated biphenyls and azo dyes. This suggests that the Sphingomonas strains have the ability to adapt environments probably by degrading compounds.

Genome analysis of S. japonicum UT26S revealed 5 replicons composed of two circular chromosomes, chromosome 1 (3,514,822 bp, 64.8 % G+C, 3,529 ORFs), chromosome 2 (681,892 bp, 65.9 % G+C, 589 ORFs) and three circular plasmids, pCHQ1 (190,974 bp, 63.0 % G+C, 224 ORFs), pUT1 (31,776 bp, 63.7 % G+C, 44 ORFs) and pUT2 (5,398 bp, 61.0 % G+C, 8 ORFs). The lin genes involved in the degradation of gamma-HCH was dispersed upon 2 chromosomes and a large plasmid. Comparison of S. japonicum UT26S genome with those of other Sphingomonadaceae strains demonstrated that about a half of lin genes were located on S. japonicum UT26S specific regions, and remaining half were embedded in conserved core regions among sphingomonad strains. These results proposed the hypothesis that lin genes were gradually acquired by S. japonicum UT26S in the course of environmental adaptation.

The genome sequence of S. japonicum UT26S should provide insights for abilities and adaptation mechanisms of pesticide degrading bacteria.

close this sectionProject history

close this date 2010-03-29 ..... 1
2010-03-29 Release of the Sphingobium japonicum UT26ST genomic sequence data
imageWe published the genomic data of Sphingobium japonicum UT26ST (= NBRC 101211) including the information of DNA clones distributed from the NBRC.

close this sectionSummary of the genomic data

SP1_2
Genomic size 4,424,862 bp
G+C content 64.85 %
Number of ORFs assigned 4,394
Percentage of the coding regions 90.62 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 9
5S16S23S
333
Number of tRNA genes 55
AlaArgAsnAspCysGln
652212
GluGlyHisIleLeuLys
231354
MetPheProSerThrTrp
313431
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
226
misc_featurerepeat_region
34192

close this sectionGeneral Procedure

The nucleotide sequence of the S. japonicum UT26S 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 5.5 kb in pUC118 vector (TAKARA) and pSMART vector (Lucigen) 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 clones were end-sequenced using dye-terminator chemistry on an ABI 3730xl DNA Analyzer (ABI).
    Fosmid end-sequencing was carried out using BaseStation DNA Fragment Analyzer BST-0100 (MJ Research Inc.).
    Sequence reads were trimmed at a threshold value of 20 by Phrap and assembled by Phrap and Consed assembly tools (http://www.phrap.org).

  • Gap closing
    Gaps between contigs were closed by sequencing PCR products which bridge two neighboring contigs.

  • Validation of the assembled sequence data
    Each base of S. japonicum genome was ensured to be sequenced from multiple clones and from both directions with Phrap quality score ≧ 70.
    In rare cases where we could not obtain sequence reads from both directions, multiple reads in the same direction with Phrap quality score ≧ 40 were also permitted if they are derived from different clones.

Gene identification and annotation
  • Putative nontranslated genes were identified using the Rfam, tRNAscan-SE and ARAGORN programs.

  • The prediction of open reading frames (ORFs) was performed using Glimmer3. The initial set of ORFs was manually selected from the prediction result in combination with BLASTP results..

  • Each ORF was annotated manually using in silico Molecular Cloning software suite (in silico biology, Inc.).

  • Putative oriC region was located using originx program.

  • Putative ORFs associated with mobile genetic elements, and their boundaries, were predicted with the great assistance of GenomeMatcher software.

close this sectionRelated links to external databases