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Actinoplanes missouriensis NBRC 102363T

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close this sectionAbout this Microorganism


Photo by Prof. Hayakawa in University of Yamanashi

Actinoplanes missouriensis strain 431T [= NBRC 102363T = DSM 43046T] is the type strain of the species A. missouriensis. Strain 431T was originally isolated from barnyard soil near Hamilton, Missouri, USA. Actinoplanes species are Gram-positive, soil-inhabiting and filamentous bacteria. The genus is of morphological interest because its members typically produce sporangia containing spores that possess flagella and are motile. Spores are released from sporangia upon contact with water and exhibit chemotactic properties. As members of Actinoplanes produce a variety of antibiotics, enzymes and other bioactive compounds, the genomes of Actinoplanes species are potentially useful genetic resources for discovering secondary metabolites and enzymes. Because strain 431T produces glucose isomerase (xylose isomerase) and has high degrading activity to flavonoid and natural rubber, this strain is expected to be useful for industrial applications.

The genome of strain 431T consists of one circular chromosome (8,773,466 bp; GC content 70.8%). A. missouriensis DSM 43046T was reported to contain a linear plasmid, pAM1, however, the corresponding plasmid was not found in strain 431Tกก(= NBRC 102363T) by CHEF electrophoresis analysis. It is possible that the linear plasmid was cured from strain 431T by repeated subculturing in the laboratory. In comparison to other members of the family Micromonosporaceae, such as Salinispora and Micromonospora, A. missouriensis has a larger genome size. Of the total of 8,204 predicted genes, 8,125 were protein-coding genes and 79 were RNA genes. More than half of the protein-coding genes (4,539, 55.9%) were assigned a putative function, while the remaining predicted genes were annotated as hypothetical proteins.

close this sectionProject history

close this date 2013-11-26 ..... 1
2013-11-26 Release of the Actinoplanes missouriensis NBRC 102363 genomic data
imageWe published the genomic data of Actinoplanes missouriensis NBRC 102363.

close this sectionSummary of the genomic data

AM2
Genomic size 8,773,466 bp
G+C content 70.82 %
Number of ORFs assigned 8,125
Percentage of the coding regions 90.77 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 18
5S16S23S
666
Number of tRNA genes 58
AlaArgAsnAspCysGln
351122
GluGlyHisIleLeuLys
341183
MetPheProSeCSerThr
513153
TrpTyrVal
114
Number of other features
(misc_RNA,misc_feature,repeat)
0

close this sectionGeneral Procedure

The nucleotide sequence of the Actinoplanes missouriensis NBRC 102363 genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE Biotechnology Center.


General Procedure
  • DNA shotgun libraries
    DNA shotgun libraries with inserts of 1.5 and 6 kb in pUC118 vector (TAKARA) was constructed.

  • Fosmid library
    A Fosmid library with inserts of 36 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 Prism 3730 sequencer (ABI).
    Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled using PHRAP/CONSED software (http://www.phrap.org).

  • Gap closing
    Fosmid end sequences were mapped onto the assembled sequence.
    Fosmid clones that link two contigs were selected and sequenced by primer walking to close any gaps.
    In some cases, Fosmid clones were subcloned by insertion of Entranceposon using Template Generation System II Kit (Finnzymes) and sequenced.

  • Validation of the assembled sequence data
    In construction of final nucleotide sequence, low-quality regions with a Phrap quality score of less than 40 were re-sequenced and verified. Finally, each base of genome was successfully ensured to be sequenced from Phrap quality value more than 40.


Gene identification and annotation
  • Putative non-translated 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.

  • For functional annotation, the non-redundant UniProt database and protein signature database, InterPro, were searched to assign the predicted protein sequences based on sequence similarities.

  • The KEGG database was used for pathway reconstruction.

  • Signal peptides in proteins were predicted using SignalP and transmembrane helices were predicted using TMHMM.


close this sectionRelated links to external databases