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Aeropyrum pernix K1T (= NBRC 100138T)

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close this sectionAbout this Microorganism


Photo by K. Yamaguchi, NBRC, NITE.

Aeropyrum pernix K1T(= NBRC 100138T) is an aerobic hyper-thermophilic archaeon and was isolated by a research team (Y. Sako et al) of Kyoto University in 1993 in a hydrothermal vent at Kodakara Island in Kagoshima Prefecture. Partly because it is an aerobic archaeon, its genome was analyzed to compare with the anaerobic P. horikoshii OT3T(= NBRC 100139T) genome. The archaeon optimally grows at temperatures between 90 to 95 C and at pH 7.0 and a salinity of 3.5% with a doubling time of about 200 min. Its growth temperature is somewhat lower than that of P. horikoshii OT3. Nonetheless it is still the highest among aerobic hyper-thermophilic archaea whose genomes have so far been analyzed. The archaeon does not require sulfur-containing compounds for growth, and hence does not generate H2S during growth.

A. pernix K1 is spherical in shape with 0.8 to 1.0 m in diameter. Similar to P. horikoshii OT3, the genome of this archaeon contains 14 tRNA genes with introns and as much as 50 % of organism-specific genes. It is interesting to note that it possesses and expresses genes encoding 'proliferating cell nuclear antigens' that play roles in the control of cell cycle, DNA-repair and apoptosis in eukaryotic organisms. These gene products were found to enhance processivity of DNA polymerases in A. pernix K1 cells. Extensive comparative analysis between P. horikoshii OT3 and A. pernix K1 and with others would reveal more interesting features associated with their genomes.

A. pernix K1 was deposited at JCM and NBRC with reference numbers of JCM 9820 and NBRC100138, respectively.

close this sectionProject history

close this date 2011-07-29 ..... 1
2011-07-29 Several information was added to Aeropyrum pernix K1T
imageWe added two feature information to Aeropyrum pernix K1T.
feature
IDlocationstatus
APE_mf0010478214..491982ADD
APE_mf0020542635..580683ADD

close this sectionSummary of the genomic data

APE
Genomic size 1,669,696 bp
G+C content 56.31 %
Number of ORFs assigned 1,700
Percentage of the coding regions 88.87 %
Percentage of the intronic regions 0.13 %
Number of rRNA genes 3
5S16S23S
111
Number of tRNA genes 47
AlaArgAsnAspCysGln
351112
GluGlyHisIleLeuLys
231152
MetPheProSerThrTrp
313441
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
20
misc_featurerepeat_region
218

close this sectionGeneral Procedure

The entire genomic nucleotide sequence of A. pernix K1 was determined by the whole genome shotgun sequencing method. It was started in April and finished in December 1998. The genome of A. pernix was completely re-annotated in May 2006. See the summary below. General Procedure
  1. Construction of a genomic physical map The physical map of the A. pernix K1 genome was constructed using three restriction enzymes, namely PacI, SgfI and SwaI. It was used for the alignment of assembled sequence data.
  2. Construction of a shotgun clone library The genomic DNA was digested by ultra-sonication and fragments of 1kb and 2kb in size were isolated and cloned into the plasmid vector pUC118. The resultant clone library was then subjected to nucleotide sequencing.
  3. Sequence data assembly The raw sequence data of the whole genome shotgun clones were assembled by using PhredPhrap and then subjected to editing with Sequencher for refinement of the assembled data.
  4. Confirmation of the edited nucleotide sequence data The assembled sequence data were used to generate PCR primers at every 15 kb intervals of the genome which were subsequently used to amplify genomic DNA fragments. Restriction enzyme maps of the resultant fragments were then compared with the one deduced from the determined nucleotide sequence.
ORF Assignment and Annotation (re-annotation)
  1. ORFs were predicted by using gene-finding programs Glimmer ver. 2.0 and GeneHacker followed by extensive manual curation.
  2. The start positions were reexamined by taking into consideration the RBS motifs based on a profile generated from the upstream regions of 130 ORFs for which start positions were experimentally determined (Yamazaki et al., 2006 a).
  3. The deduced protein sequences were subjected to BLASTP (Altschul et al., 1997) search against Swiss-Prot/TrEMBL database and were analyzed by InterPro program (Mulder et al., 2003).
  4. Signal peptides were predicted by SignalP program (Bendtsen et al., 2004), and transmembrane regions were predicted by TMHMM program (Krogh et al., 2001).
  5. Ribosomal RNA sequences were modified according to the reference (Nomura et al., 1998).
  6. Transfer RNAs were first predicted by using tRNAScan-SE and Infernal software with Rfam database and then refined by adding intron information according to the reference (Yamazaki et al., 2006 b).
Summary of the A. pernix Genomic Data
    The genomic data of A. pernix was changed as follows.
    1. Genomic size: 1,669,695 bp -> 1,669,696 bp (single bp insertion at position 941,216)
    2. ORFs:
      1. Number of ORFs: 2,694 -> 1,700
      2. Number of ORFs changed in N-terminus: 978
      3. Number of deleted ORFs : 1,128
      4. Number of newly added ORFs : 134
Genomic size: 1,669,696 bp
GC content: 56.3 %
Number of ORFs assigned: 1,700
Coding region coverage: 88.8 %
5S, 16S and 23S rRNA genes: 1 each
srpRNA gene: 1
tRNA genes: 47
Repeat sequences: 15

close this sectionRelated links to external databases