Figure 4

Qualitative UV assay and mRNA analysis of E. coli R391 mutants KOA, KOB and KOC. (A) AB1157 R391 mutants KOA, KOB and KOC. UV_254nm exposure increasing (12 J.m^-2) from left to right. (i) From top to bottom, AB1157, AB1157 R391, AB1157 R391 KOA. (ii) AB1157, AB1157 R391 KOB. (iii) AB1157, AB1157 R391, AB1157 R391 KOC. (B) SYBR® Safe stained 1% (w/v) agarose gel confirming orf43 mRNA transcription in AB1157 R391 KOA. M, Bioline Hyperladder I DNA marker; 1, AB1157 R391 RNA negative control; 2, AB1157 R391 genomic DNA positive control; 3, AB1157 orf43 cDNA; 4, AB1157 R391 orf43 cDNA; 5, KOA orf43 cDNA; 6, KOB orf43 cDNA; 7, KOC orf43 cDNA; 8, KOB orf20 cDNA. Primers used specific to orf43 generated a 188 bp PCR product. Primers used for lane 8 only were specific for the kanamycin resistance gene of ICE R391, orf20, which generated a PCR product of 223 bp. Amplification of orf20 specific cDNA was carried out to show KOB and KOC RNA was not degraded. Lane 1 negative control was DNase treated RNA that was not converted to cDNA. (C) Map of exact locations of KOA, KOB and KOC deletions on ICE R391 genome. The KOA, KOB and KOC ampicillin resistance cassettes and associated promoter were inserted into the ICE R391 genome in the reverse complement to prevent the ampicillin resistance cassette promoter inducing the transcription of orf43 mRNA. The KOA deletion removed all possible promoters of orf43 in front of the gene and left the last 36 bp specific to the preceding orf42 gene. The KOB deletion removed the same region as KOA and the 36 bp region. The KOC deletion was a duplicate of KOA with an additional zeocin resistant orfs90/91 deletion.