For E. coli KOEGE 118 and KTE 9 which harboured two dnd-encoding GIs within the same genome, their respective dnd-encoding GIs were also associated with different tRNA genes (leu and thr tRNA genes).
In addition, via in silico analysis, dndDB identified 26 syntenic dnd clusters from 25 species of Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid containing 114 dnd genes.
This phenomenon is due to a DNA phosphorothioate modification conferred by a cluster of five dnd genes which are only present in the S.lividans genome in the 93 kb island [ 13, 17- 19].
A total of 106 positive hits (with BLASTN e-value = 0, identity ≥ 85% and coverage ≥98%) were obtained from both databases of non-redundant nucleotide collection (nr/nt) and whole genome shotgun contigs (WGS) using the three dnd operons (E. coli SE11, 55989 and B7A) as queries.
Some bacterial species harboured a 4-gene dndBCDE operon whereas others carried a five-gene dnd cluster (dndA and dndBCDE operon).
The three complete dnd operons of Dnd+ E. coli strains (B7A, 55989 and SE11) available from dndDB (dnd database, http://db-mml.sjtu.edu.cn/dndDB) were used as query sequences because the dnd operons as well as their association with genomic islands (GI) have been reported [ 10].
Asterisks indicate that the genome contains two copies of dnd operons.
We design and fabricate two kind of DNDs: one with a linear modulator (l-DND) and the other with nonlinear modulator (n-DND), both having an identical input and output strokes of 15.2 μm and 5.4 μm, respectively.
Seven of the Dnd+ strains were verotoxigenic- E. coli (VTEC) isolated from different piglets in the same swine farm.
