High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates
(A) cDNAs reads of TEX−/+ libraries mapped to the CRISPR loci in C. jejuni NCTC11168. TSS are marked by black arrows. A −10 box for each crRNA is present in the 3′ part of the corresponding upstream located repeat (blue box). The lower panel shows the potential base-pairing of C. jejuni TracrRNA with the repeat sequence. (B) Northern blot analysis of TracrRNA and crRNAs. Total RNA (15 µg per lane) extracted from C. jejuni strains at mid-exponential (E), stationary (S), and overnight (O) growth phase was analyzed on a Northern blot using labeled DNA probes complementary to TracrRNA (two upper panels) and crRNA2 in NCTC11168 (see Table S14). Both the mature (∼62 nt) and processed (∼74 nt) TracrRNA forms as well as intermediate (∼103 nt) and mature (∼38 nt) crRNA forms for crRNA2 in NCTC11168 were detected. 5S rRNA served as loading control. (C) Conservation of CRISPR loci in different Campylobacter jejuni strains. In strain RM1221, cas9 contains a premature-stop mutation. In strain 81–176 the whole CRISPR locus is replaced by two genes (green arrows) with low G/C-content. (D) Subclassification of type-II CRISPR-loci. cas9, cas1, and cas2 are indicated with blue arrows and tracrRNA by a red box, respectively. TSS upstream of the repeat (black squares)-spacer (green diamonds) units in type-II A and B CRISPR loci ,  or within each spacer in the case of the minimal type-II C CRISPR systems of Campylobacter jejuni (CJ) and Neisseria meningitidis (NM) are marked by black arrows. Representative species for each type-II class are listed (SP: Streptococcus pyogenes, ST: S. thermophilus, TD: Treponema denticola, LI: Listeria innocua, and LP: Legionella pneumophila).