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Acidiphilium multivorum AIU301 (= NBRC 100883)

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close this sectionAbout this Microorganism


Photo by Dr. Uchino (NBRC, NITE)

Acidiphilium multivorum AIU301T was isolated as an acidophilic, aerobic, anoxygenic and phototrophic bacterium from pyritic acid mine drainage. Members of the genus Acidiphlium belonging to alpha-proteobacteria are well known to have high ability of resistance to various metals under acidic condition, and require high acidity for growth. A. multivorum AIU301T is also characterized as a strain exhibiting tolerance to nickel, zinc, cadmium and copper ion. Furthermore, A. multivorum AIU301T exhibits resistance to arsenate and arsenite. Also interesting is that A. multivorum AIU301T has zinc-chelated-bacteriochlorophylls (Zn-Bchl) a rather than Mg-Bchl a as the major photopigment. This unique character is limited in a group of aerobic acidophilic proteobacteria including species of the genus Acidiphlium.

Genome analysis of A. multivorum AIU301T revealed nine replicons composed of one circular chromosome (3,749,411 bp, 67.6% G+C, 3,449 ORF) and eight circular plasmids pACMV1 (271,573 bp, 62.9% G+C, 284 ORF), pACMV2 (65,564 bp, 61.9% G+C, 69 ORF), pACMV3 (54,248 bp, 61.2% G+C, 61 ORF), pACMV4 (40,588 bp, 60.1% G+C, 44 ORF), pACMV5 (14,328 bp, 59.0% G+C, 19 ORF), pACMV6 (12,125 bp, 59.6% G+C, 14 ORF), pACMV7 (5,178 bp, 57.6% G+C, 8 ORF) and pACMV8 (1,728 bp, 60.9% G+C, 1 ORF). The chromosome and circular plasmids encode many genes which seem to be involved in heavy metal-transport, and three operons which seem to contribute to arsenic resistance. A. multivorum AIU301T chromosome showed overall high conservation of synteny with Acidipphilium cryptum JF-5 chromosome which has been sequenced, excluding a few regions. One of the unique regions that exist only in A. multivorum AIU301T is a 225-kb region which contains the photosynthesis gene cluster and many insertion sequences.

The genome sequence of A. multivorum AIU301T would provide insights into the understanding of acidophilic bacteria, and may also facilitate the development of technologies utilizing this bacterium such as bioremediation in acidic and metal-rich environment.

close this sectionProject history

close this date 2011-03-29 ..... 1
2011-03-29 Release of the Acidiphilium multivorum AIU301T genomic data
imageWe published the genomic data of Acidiphilium multivorum AIU301 (= NBRC 100883).

close this sectionSummary of the genomic data

AM1
Genomic size 4,214,744 bp
G+C content 66.97 %
Number of ORFs assigned 3,949
Percentage of the coding regions 90.93 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 6
5S16S23S
222
Number of tRNA genes 48
AlaArgAsnAspCysGln
441112
GluGlyHisIleLeuLys
241242
MetPheProSerThrTrp
413431
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
462
repeat_region
462

close this sectionGeneral Procedure

The nucleotide sequence of the A. multivorum AIU301T (= NBRC 100883T) 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 1.7, 6.0 kb in pUC118 vector (TaKaRa)/pSMART-LCKan (Lucigen) was constructed.

  • Fosmid library
    A Fosmid library with inserts of 35 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). Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled by PHRAP/CONSED software (http://www.phrap.org).

  • Gap closing
    To close gaps , it selected shotgun or fosmid clones bridging two neighboring contigs and determined their internal sequences by the primer-walking method using custom oligonucleotide primers or the transposon-mediated random insertion method with a Template Generation System II Kit(Finnzyme).

  • Validation of the assembled sequence data
    The assembled sequence was validated by gel electrophoresis, restriction enzyme digestion of fosmid clone and Optical Mapping system (OpGen). Finally, each base of A. multivorum AIU301 genome was ensured to be sequenced from multiple clones with Phrap quality score íŠ 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 program was used. The initial set of ORFs was manually selected from the prediction result in combination with BLASTP.

  • Similarity search results against Uniprot, Interpro and HAMAP database were used for functional prediction. The KEGG database was used for pathway reconstruction.


close this sectionRelated links to external databases