ISPze1

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
GU826202 Y Paracoccus zeaxanthinifaciens
Paracoccus zeaxanthinifaciens ATCC 21588T
DNA section
IS Length : 851 bp

Ends


IR Length : 13/18

IRL : GGGTCAGGACCCATTAATTTTCTTGATGCCGTCCTGTCGGCGTGATTCAC
IRR : GGCTCCAGACTCATTGATGGTCACAGCCAGAACATGACGGTGGCAGCGAG

Insertion site


Left flankDirect repeatRight flankDR Length
GACGGCTGCATACTAACCGCTT2

DNA sequence

GGGTCAGGACCCATTAATTTTCTTGATGCCGTCCTGTCGGCGTGATTCACGCTCCCAAACAGGTGGGGGCATCATGAGTAATCTTTTCTGGCTGACGGAC
GAACAGATGGAGCGGCTGAAGCCGTTCTTCCCCAAGAGCCATGGTAAGCCGAGGGTCGATGACCGGCGCGTGCTGAGCGGCATAATCTTCATCAACCGCA
ATGGGTTGCGGTGGTGCGATGCGCCCCGGGAGTATGGCCCGCCCAAGACGCTCTACAACCGGTGGAAGCGCTGGAGCGAGATGGGCGTGTTTGCCAGGAT
CTTCGAGGGATTGGCCTCGGAGGCAACGGATCAGAAGACGCTGATGATTGATGCGACGTATCTGAAAGCCCATCGCACGGCGTCGAGCCTGCGGTCGAAA
AAGGGGGGCGTGGACGCCTGATTGGCAGGACTAAGGGCGGTATGAACACCAAGTTGCATGCCGTCACGGATGCCAGAGGCCGCCCACTCAAGTTTTTCAT
GACGGCCGGCCAAGTCAGCGATTACACCGGTGCAGCCGCGCTGCTGAGCAGCCTGCCTCGGGCGGACTGGCTGCTCGCCGACCGAGGCTATGATGCGGAT
TGGTTCCGCGACGCCCTGAAAGACAAGGGGATCAGGCCCTGCATCCCGGGCCGGAAGTCCCGCGGCAAGCCCGTCAAATACGACAAGCGACGCTACAGAC
GACGCAACCGCATAGAGATCATGTTCGGTAGGTTGAAGGACTGGCGGCGAGTAGCGACACGTTACGATAGATGCCCAAAGGTCTTCCTCTCCGCCGTCGC
TCTCGCTGCCACCGTCATGTTCTGGCTGTGACCATCAATGAGTCTGGAGCC
Recoding section
  • Recoding by frameshift
  • Frame
  • Type
  • Experimentally demonstrated

Stimulators :

  • Shine-Dalgarno sequence :
  • Secondary structure :

Recoding motif :

Protein section
ORF number : 3

 

ORF 1
LengthBeginEndStrandFusion ORF
348 bp115 aa74421+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSNLFWLTDEQMERLKPFFPKSHGKPRVDDRRVLSGIIFINRNGLRWCDAPREYGPPKTLYNRWKRWSEMGVFARIFEGLASEATDQKTLMIDATYLKAH
RTASSLRSKKGGVDA

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
480 bp159 aa352831+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

CDVSESPSHGVEPAVEKGGRGRLIGRTKGGMNTKLHAVTDARGRPLKFFMTAGQVSDYTGAAALLSSLPRADWLLADRGYDADWFRDALKDKGIRPCIPG
RKSRGKPVKYDKRRYRRRNRIEIMFGRLKDWRRVATRYDRCPKVFLSAVALAATVMFWL

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
758 bp252 aa74831+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSNLFWLTDEQMERLKPFFPKSHGKPRVDDRRVLSGIIFINRNGLRWCDAPREYGPPKTLYNRWKRWSEMGVFARIFEGLASEATDQKTLMIDATYLKAH
RTASSLRSKKGGRGRLIGRTKGGMNTKLHAVTDARGRPLKFFMTAGQVSDYTGAAALLSSLPRADWLLADRGYDADWFRDALKDKGIRPCIPGRKSRGKP
VKYDKRRYRRRNRIEIMFGRLKDWRRVATRYDRCPKVFLSAVALAATVMFWL

 

Blast result :
Comments
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPze1 (orfAB) is 93% aa similar to ISPak1.
ISPze1 has been identified by its transposition into entrapment vector pMEC1 (cI-tetA cassette). ISPze1 is 83% (ORF1) aa identical to ISPam4, 81% (ORF2) to ISPam4. At position 398, ISPze1 carries the sequence 5'-AAAAAG-3' that might function as a -1 translational frameshifting site. IRL of ISPze1 contains a sequence 5’-AATTTTcTTGAT -3’ matching (1 mismatch) to consensus sequence of integration host factor (IHF) binding site 5’-AANNNNTTGAT-3’. As judged from DNA hybridization analysis ISPze1 is present in 6 copies in the genome of Paracoccus zeaxanthinifaciens ATCC 21588T. Homologous sequences were also detected by DNA hybridization in P. aestuarii DSM 19484, P. denitrificans DSM 413, P. haeundaensis LMG P-21903, P. halophilus JCM 14014, P. homiensis DSM 17862, P. kondratievae NCIMB 13773T, P. koreensis JCM 21670, P. pantotrophus DSM 11072, P. pantotrophus DSM 11073, P. pantotrophus DSM 65, P. pantotrophus LMD 82.5, P. seriniphilus DSM 14827, P. solventivorans DSM 11592, P. solventivorans DSM 6637, P. versutus UW 1, P. yeei CCUG 46822.
References
1] Dziewit, L. and Bartosik, D. (2010) Direct submission
2] Dziewit, L., Baj, J., Szuplewska, M., Maj A., Tabin, M., Czyzkowska, A., Skrzypczyk, G., Adamczuk, M., Sitarek, T., Stawinski, P., Tudek, A., Wanasz, K., Wardal, E., Piechucka, E., Bartosik, D. (2012) PLoS ONE 7: e32277