ISPaes2

  • Family IS5
  • Group IS427
MGE type ISRelated element(s) :
Isoform Synonym(s)
Accession numberTranspositionOriginHost
GU826198 Y Paracoccus aestuarii
Paracoccus aestuarii DSM 19484
DNA section
IS Length : 841 bp

Ends


IR Length : 18/21

IRL : GGCTCCAGACCCATTGATCTTACGGTCTTTGCATGATTCATGCTCCTCAA
IRR : GGCTCCAGACTCATTAAGTTTCACAGCCAGAACAAGACGGTTGCGGCGAG

Insertion site


Left flankDirect repeatRight flankDR Length
GCATTACGTCTAACGATATTTA2

DNA sequence

GGCTCCAGACCCATTGATCTTACGGTCTTTGCATGATTCATGCTCCTCAAGGAGACCTGATCGATGAGTAATCTTTACTGGCTGAGCGACGCCCAAATGG
AGCGTCTGAAACCGTTCTTTCCCAAGAGCCATGGCAAGCCCCGGGTCGATGATCGTCGCGTCCTCAGCGGCATAATTTTCATCAATCGTAATGGGTTGCG
GTGGTGTGACGCGCCGAAGGAATACGGCCCGGCCAAAACCCTCTACAACCGCTGGAAGCGCTGGAGCGATAACGGGGTTTTTGCCCGGATCATTGTCGGC
CTTGCCGCCGAGAGCGCCGAGCACAAGACGATCATGATTGACGCGACCTATCTCAAGGCACACCGCACGGCCTCGAGCCTTGGGGTGAAAAAGGGGGGCG
CGGGCGCCAGATCGGGCGCACCAAAGGCGGTATGAACACCAAGTTGCACGCTGTCGCCGATGCGAAGGGGCGGCCGATCGGGTTCTTCATGTCGGCCGGC
CAGGTTAGCGATTACACCGGCGCGGCGGCGCTGCTGGGCAGCCTGCCGAAGGCTGAGTGGCTTCTGGCCGACAGGGGCTACGACGCTGATTGGTTCAGAG
ACGCTTTGAAAGACAAGGGGATAAAGGTTTGCATCCCCGGACGGAGGTCCCGCAAGAAGGTCGTCAAATACGACAAGCGGCGTTACAAAAGGCGTAACCG
CATCGAAATCATGTTCGGACGTCTGAAGGACTGGAGGCGCGTCGCAACCCGTTATGACCGCTGCCCGGAAACGTTCTTCTCAGCGATCATGCTCGCCGCA
ACCGTCTTGTTCTGGCTGTGAAACTTAATGAGTCTGGAGCC
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
372 bp123 aa64435+No
ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSNLYWLSDAQMERLKPFFPKSHGKPRVDDRRVLSGIIFINRNGLRWCDAPKEYGPAKTLYNRWKRWSDNGVFARIIVGLAAESAEHKTIMIDATYLKAH
RTASSLGVKKGGAGARSGAPKAV

 

Blast result :
ORF 2
LengthBeginEndStrandFusion ORF
480 bp159 aa342821+No
ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

RDLSQGTPHGLEPWGEKGGRGRQIGRTKGGMNTKLHAVADAKGRPIGFFMSAGQVSDYTGAAALLGSLPKAEWLLADRGYDADWFRDALKDKGIKVCIPG
RRSRKKVVKYDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPETFFSAIMLAATVLFWL

 

Blast result :
ORF 3
LengthBeginEndStrandFusion ORF
758 bp252 aa64821+Yes
ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSNLYWLSDAQMERLKPFFPKSHGKPRVDDRRVLSGIIFINRNGLRWCDAPKEYGPAKTLYNRWKRWSDNGVFARIIVGLAAESAEHKTIMIDATYLKAH
RTASSLGVKKGGRGRQIGRTKGGMNTKLHAVADAKGRPIGFFMSAGQVSDYTGAAALLGSLPKAEWLLADRGYDADWFRDALKDKGIKVCIPGRRSRKKV
VKYDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPETFFSAIMLAATVLFWL

 

Blast result :
Comments
The third ORF is a putative ORFAB transposase reconstructed in silico by a possible -1 frameshift.
ISPaes2 is 92% (ORF1) aa identical to ISRhsp4, 82% (ORF2) to ISSpo7.
ISPaes2 has been identified by its transposition to the entrapment vector pMAT1 (sacB cassette). At position 388, ISPaes2 contains a sequence 5'-AAAAAG-3' that might function as a -1 translational frameshifting site. IRL of ISPaes2 contains a sequence 5’-gACCCATTGAT -3’ matching (1 mismatch) to consensus sequence of integration host factor (IHF) binding site – 5’-AANNNNTTGAT-3’. As judged from DNA hybridization analysis ISPaes2 is present in 2 copies in the genome of P. aestuarii DSM 19484. Homologous sequences were also detected by DNA hybridization in P. alcaliphilus JCM 7364, P. alkenifer DSM 11593, P. aminophilus JCM 7686, P.aminovorans JCM 7685, 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. marcusii OS 22, P. methylutens DM 12, P. pantotrophus DSM 11072, P. pantotrophus DSM 11073, P. pantotrophus DSM 65, P. pantotrophus LMD 82.5, P. solventivorans DSM 11592, P. solventivorans DSM 6637, P. thiocyanatus JCM 20756, P. versutus UW 1, P. yeei CCUG 32052, P. yeei CCUG 32053, P. yeei CCUG 46822, P. zeaxanthinifaciens ATCC 21588¬T.
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