New type I toxin-antitoxin families from “wild” and laboratory strains of E. coli

Figures & data

Figure 1. Ibs-Sib loci in E. coli MG1655. (A) Genetic organization of the loci. (B) Alignment of the five sib gene sequences from E. coli MG1655. The Target Recognition Domains (TRD1 and TRD2) are indicated as determined by Han, et al.¹⁶

Figure 2. ShoB-OhsC locus of E. coli MG1655. (A) Genetic organization of the locus. Note the arrow for shoB indicates the mRNA; the box within the arrow indicates the coding region of the sequence. (B) Base pairing between shoB and OhsC. (C) Predicted secondary structure of shoB.²⁸ The start codon is boxed; the predicted ribosome binding site is indicated by the dashed bracket; the region of base pairing to OhsC is indicated by the bracket.

Figure 3. Zor-Orz locus of E. coli O157:H7 str. EDL933. (A) Genetic organization of the locus. Note the arrows for zorO and zorP indicate the mRNAs; the boxes within the arrows indicate the coding region of the sequences. (B) Base pairing between zorO and OrzO. (C) Predicted secondary structure of zorO.²⁸ The start codon is boxed; the predicted ribosome binding site is indicated by the dashed bracket; the region of base pairing to OhsC is indicated by the bracket.

Table 1. Distribution of selected type I toxin loci across selected species^a.

Locus	E. coli MG1655^b.	E. coli DH10B^b.	E. coli CFT073^c.	E. coli O157:H7 str. Sakai^c.	E. coli SE11^d.	E. coli IAI1^d.	Shigellaboydii Sb227^c.	Salmonella enterica Typhy Ty2^c.	Hemophilus somnus 2336^c.
Ibs-Sib	5	5	4	7	7	7	7	2	7
ShoB-OhsC	1	1	1	1	1	1	1	0	0
Zor-Orz	0	0	1	2	2	2	1	0	0

^a Data from Fozo et al. 2010. ^bLaboratory strain. ^cPathogenic strain. ^dCommensal isolate.

Han K, Kim KS, Bak G, Park H, Lee Y. Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family. Nucleic Acids Res 2010; 38:5851 - 66; http://dx.doi.org/10.1093/nar/gkq292; PMID: 20453032

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Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31:3406 - 15; http://dx.doi.org/10.1093/nar/gkg595; PMID: 12824337

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