ISX' and ISZ'

Description:

ISX' is a 312 bp IS3 family partial IS element present in single copy at 6'.
insX' is the 5' partial pseudogene of an IS3 family transposase A encoded in ISX'.
ISX' is in the compound IS1B-IS30B-ISX' cluster in the putative defective prophage CP4-6.

ISZ' is a 989 bp IS4 family partial IS element present in single copy at 27.9'.
insZ' has two frameshifts and is apparently deleted for an internal fragment (~450 bp).
ISZ' has inserted between the convergent tdk and adhE genes.

ISZ' has an 18 bp imperfect inverted repeat at its ends, 1-18 (1294628-1294611, CAATGCCGATCAGTTAAG) is the reverse complement (16/18) of 1408-1426 (1293657-1293640, CTTAAGTGAACGGCATTG) , which includes the TGA stop codon of insZ'.

Details:

E. coli K-12 strain MG1655 contains two instances of apparently defective novel IS elements.


IS LeftEnd RightEnd Ori Comments

ISX' 280114 280425 (-) Interrupts yagB', IS3 family, ISEhe3-like
ISZ' 1294426 1295405 (-) Contains IS4 transposase family pseudogene insZ'
ISZ'

ISZ' was identified and named previously (Rudd, 1998), and updated ISZ' annotations are presented in EcoGene.

The mismatched bases in the terminal inverted repeats are emboldened:

CAATGCCGTTCACTTAAG ISZ' LE (+)
CAATGCCGATCAGTTAAG ISZ' RE (-)
The chromosomal right end of ISZ' (1294594-1294628) is a 33/35 match to the chromosomal right end of IS4 (4501504-4501538), including a 17/18 match to the IS4 inverted repeats.

The chromosomal left end of ISZ' has a 15/18 bp match to the IS4 terminal inverted repeat and matches 16/18 with the reverse complement of the right end of ISZ', clearly marking the ends of ISZ'.
The ends of ISZ' and its IS4-like nature are corroborated by finding a 10 bp perfect target site duplication, CCCAGAAGGG, immediately flanking the ends of ISZ'.

CAATGCCGTTCACTTAAG ISZ' LE (+)
CAATGCCGATCAGTTAAG ISZ' RE (-)
TAATGCCGATCAGTTAAG IS4 18 bp terminal IR
The mismatched bases are depicted in bold, and coincidentally flank the insZ' stop codon on the opposite strand in ISZ' LE.

The chromosomal right end (begining) of ISZ'(-) is annotated about 80 nt upstream of the start codon for insZ', similar to the distance upstream of insG on IS4.


ISX'

ISX' was identified and named previously (Rudd, 1998), and updated ISX' annotations are presented in EcoGene.

ISX' is 94% identical to the first 313 bp of the 1237 bp ISEhe3 element in Genbank AF327445 (Guo, 2002).
"ISY", from 271415 273178 (+) was previously predicted to be a novel IS element (Rudd, 1998), but the term ISY has now been dropped and the source of the retron-type reverse transcriptase family pseudogene ykfC' in the CP4-6 prophage is unknown.