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Sulfolobus tokodaii strain 7T (= NBRC 100140T)

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close this sectionAbout this Microorganism


Courtesy of Dr. Wakagi (formerly Oshima Lab., Mitsubishi Chemical Corp.)

This archaeon was isolated from one of the hot springs in Beppu-Onsen of Oita Prefecture. It is capable of decomposing hydrogen sulfide by itself and grows well under acidic conditions. It belongs to Crenarchaeota as in the case of Aeropyrum pernix K1T(= NBRC 100138T), but its genome (2.69 Mb) is about 1 Mb larger than that of A. pernix K1. The larger genome size is most probably due to the integration of a plasmid during the course of evolution, since as many as 81 genes/ORFs assigned on the genome of this archaeon show similarity to those encoded in a plasmid present in another species of Sulfolobus. In addition, the archaeon seems to contain duplications of many genes/ORFs.

Unlike the two other archaea previously analyzed at NITE-DOB, i.e. P. horikoshii OT3T(= NBRC 100139T) and Aeropyrum pernix, the genome of this archaeon does not seem to contain genes encoding proteins with inteins. Furthermore, it contains as many as 14 genes/ORFs that show similarity to eukaryotic genes including those encoding a eukaryotic type of selenium-binding protein, a serine/threonine protein phosphatase subunit, etc. Since these genes/ORFs could not be detected in the genomes of other archaea, S. tokodaii strain 7 is likely to be more closely related to eukaryotes than other archaea so far analyzed.

close this sectionProject history

close this date 2012-05-15 ..... 1
2012-05-15 Update of proteome analysis result of Sulfolobus tokodaii 7T
imageWe have updated gene assignment of 2 CDS based on N-terminal amino acid sequencing result.

Changed ORFs
IDold locationnew locationstatus
STK_09620938120..937341938195..937341CHANGE
STK_127501274212..12736851274272..1273685CHANGE

close this sectionSummary of the genomic data

ST
Genomic size 2,694,756 bp
G+C content 32.79 %
Number of ORFs assigned 2,816
Percentage of the coding regions 84.67 %
Percentage of the intronic regions 0.02 %
Number of rRNA genes 3
5S16S23S
111
Number of tRNA genes 46
AlaArgAsnAspCysGln
351112
GluGlyHisIleLeuLys
231152
MetPheProSerThrTrp
313431
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
46
repeat_region
46

close this sectionGeneral Procedure

Procedure of analysis
  1. Construction of the whole genome shotgun (WGS) clones The whole genomic DNA of S. tokodaii strain 7 and fragments obtained by digesting it with BssH II were used for the construction of shotgun clone libraries. The genomic DNA was fragmented by sonification and the resultant fragments of 0.8 to 1.2 kb and of 2.0 to 2.5 kb in size were independently cloned into the Hinc II site of pUC118.
  2. Sequencing Plasmid DNA obtained by running an Autogen 740 automatic DNA preparation system was used for cycle sequencing reaction and subjected to analysis by ABI-DNA sequencers. After WGS clone sequencing and data assemble, the remaining sequencing gaps were filled by PCR walking using primers synthesized based on the sequence data. Assembly and editing of the sequence data were performed by Phred/Phrap/Consed and Sequencher.
  3. Analysis of the sequence data ORFs were assigned and similarity search was mainly performed by using the Smith-Waterman algorithm. The databases used for similarity search were Genbank release 109, EMBL release 56.0, Swiss-Prot release 38.0, PIR release 62.0 and Owl release 31.4.

Gene identidication and annotation
  • For the prediction of protein-coding genes, Glimmer3 and GeneMark programs were 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.


close this sectionRelated links to external databases