23E6

Site of transposon insertion cloned as PstI fragment into pSP72. 
Sequenced in opposite orientations with JEP131 and JEP132,
from sites at opposing ends of the transposon, to give:

JEP131 413 bp

JEP132 416 bp

 
Composite sequence:

NCGNGAAGCC GCCACCAGCG GAATGCCCGG CACCATGGCG TAGATCAGAT
AACCGACGCC GNCCACGGTG ATCAACACCA GCACCAGCGC CAGGCCGAGA
ATTTCACGCC CGTGATGCAG GAACTCGCGC GTCGGCGTTT TCCAGCCGTC
GGCGAACAGC AGCGGCGGGA TGAACAGCAC CAGGAACAGT TCGGGATCAA
AGTCGACGTG CAGCCCGAAA TGCGGCCAGG CCAACAGGGC CCCGATGGCG
ATTTGCATCA GCGGCAGCGG CACCTGGAAC GGCAACATGC GCGTCACCAC
CCCGGACAGG GAGACCACCA GGATCAAAAT GAGGATTGTA AAAAAGATTT
CCATGCTTTC CTTAGACTCT ACGATTCAGA CGACATCGGC TCAGGGCCTG
CGTGNGGCNT NGA

NGNANANGGT CCCGATAGTA GATCACTTTT TTTACAGCCG TTAAAGCTTG
TTGTGCCTTT CAAAACGCGG TGCAGAGCAG AAGAAGACTT ATCTTAAGAA
AGGGAATTGC CGTCACAGGC TCCCCCGCCC GATGGGCGAG GGAAACCCAA
GAGGCTTAAA TCGCCCAGCC GCCGGCGTAG AACGCCACCA GCGCCACGGC
GATCAGCACG GTGCCGATGT TCAACTTGCG CCATTCGCCG GAGAAGATGC
GGCCGATGAC CAGCGAGCTG AAGCCCAGCA TGATGCCGGT GACGATGTTG
CAGGTCAGCA CGATGAACAC CGCGCACAGC AGGCCGGCCA TTGCGTCGAC
GAAGTCGTTG AAGTCCAGCT TGGTGACGTT GCTCAGCATC AGCAGGCCGA
CGTACATCAG CGCCGG




BLASTX with this sequence gives hits to a family of proteins (full results here), 
with the top hit being extremely conserved:


>gi|16123771|ref|NP_407084.1| (NC_003143) putative xanthine/uracil permease [Yersinia pestis]
          Length = 451

 Score =  162 bits (409), Expect = 1e-39
 Identities = 79/86 (91%), Positives = 84/86 (96%)
 Frame = -1

Query: 829 PALMYVGLLMLSNVTKLDFNDFVDAMAGLLCAVFIVLTCNIVTGIMLGFSSLVIGRIFSG 650
           PALMYVGLLMLSNV+KLDF DFVDAM+GLLCAVFIVLTCNIVTGIMLGFSSLVIGR+ SG
Sbjct: 366 PALMYVGLLMLSNVSKLDFEDFVDAMSGLLCAVFIVLTCNIVTGIMLGFSSLVIGRVCSG 425

Query: 649 EWRKLNIGTVLIAVALVAFYAGGWAI 572
           EWRKLN+GTV+IAVALVAFYAGGWAI
Sbjct: 426 EWRKLNVGTVIIAVALVAFYAGGWAI 451




Taking the first 576 bp of the sequence, one obtains these results, with the top hit being:


>gi|16123772|ref|NP_407085.1| (NC_003143) putative  putative Na(+)/H(+) exchanger protein
           [Yersinia pestis]
           Length = 549

 Score =  108 bits (271), Expect = 2e-23
 Identities = 57/95 (60%), Positives = 60/95 (63%)
 Frame = -3

Query: 291 RMLPFQVPLPLMQIAIGALLAWPHFGLHVDFDXXXXXXXXXXXXXFADGWKTPTREFLHH 112
           RMLPFQVPLPLMQI  GALLAWP+FGLHV+FD             FADGWKTPTREF+HH
Sbjct: 22  RMLPFQVPLPLMQIVCGALLAWPNFGLHVNFDPELFLVLFIPPLLFADGWKTPTREFIHH 81

Query: 111 GREXXXXXXXXXXXXXXXXXXXIYAMVPGIPLVAA 7
           GRE                   IY MVPGIPLVAA
Sbjct: 82  GREILGLALALVLVTIVGIGYLIYWMVPGIPLVAA 116

The transposon is thus inserted 3' of a homologue of YPO3629 and 5' of a homologue of YPO3630. The former is a putative xanthine/uracil permease, homologous to the E. coli YjcD, and the latter protein is homologous to the E. coli putative Na(+)/H(+) exchanger YjcE.

Surprisingly, STRING analysis does not recognise that either of these genes or their orthologues occur repeatedly with certain genes in one gene cluster.

Colibri shows that yjcD and yjcE are flanked on one side by genes of unknown function and on the other by soxS and soxR. The sox regulon contains at least 15 proteins and is induced when superoxide levels increase. This stress response is apparently complex and is partly dependent upon iron availability.

See also the entries for yjcD and yjcE at EcoGene

For the putative Na(+)/H(+) exchanger YjcE Verkhovskaya et al. reported that:

"Two genes in the Escherichia coli genome, b4065 (yjcE) and b1191 (ycgO), are similar to genes encoding eukaryotic Na(+)/H(+) exchangers. Mutants were constructed in which yjcE (GRN11), ycgO (GRF55) or both (GRD22) were inactivated. There was no change in respiration-driven Na(+) efflux in any of the mutants when grown in media containing 50-500 mM Na(+). The only striking finding was that growth of GRF55 was impaired at low osmolarity. In complex low-salt medium, GRF55 grew at a wild-type rate for three to four generations but then stopped; the growth was partially recovered after a pause, the length of which was dependent on salt concentration. Measurement of cytoplasmic alkali cations showed that an abrupt loss of about one-half of the intracellular K(+) preceded the pause. When grown in low-salt medium with only 20 mM added Na(+), GRF55 also lost the ability to maintain a sodium concentration gradient. However, this phenomenon appears to be a secondary effect of the ycgO deletion. The double mutant GRD22 has the same properties as GRF55; no additional effect was found. The data indicate that neither ycgO nor yjeE participates in respiration-driven Na(+) extrusion. Instead, ycgO is required for growth at low osmolarity." ['yjeE' is presumably a typographical error for 'yjcE']