Metris et al. BMC Genomics 2011, 12:535 http://www.biomedcentral.com/1471-2164/12/535 Page 5 of 14 pseI maf1 cj1319 cj1320 cj1321 cj1322 cj1323 cj1324 cj1325 neuB2 neuC2 cj1329 cj1330 ptmB ptmA pseD maf3 maf4 pseE Putative Non-essential gene Putative Essential gene Mariner transposon insert site Tn7 transposon insert site Pseudogene showing stop codons Polymorphism (G/C)n cj0501 hemH cj0504c cj0505c alaS maf pbpA clpB cj0510c cj0511 cj0889c cj0890c serA cj0892c rpsA ispH aroA pheT pheS cj0898 thiJ cj0900c cj0901 glnQ Figure 1 Circular representation of the C. jejuni NCTC11168 genome showing positions of transposon inserts. Outer 2 circles: open reading frames (purple) and pseudogenes (black) on the forward and reverse DNA strands. The next two circles show insert positions based on the Mariner library (dark red) and the Tn5 library (light red). The innermost circle shows %GC. Numbers on the outermost circle show the base number with respect to the start of dnaA (cj0001). Box outs show examples of the transposon mutagenesis analysis (genes are not drawn to scale). Genes are predicted essential if they lack any transposon insert (e.g. alaS or aroA) while genes with an insert are predicted to be dispensable for growth under laboratory conditions. The upper box out shows a region of the genome densely populated by transposon inserts and therefore this whole region is likely dispensable for growth under laboratory conditions. This region of the chromosome encodes functions relating to cell envelope biosynthesis and flagella modification. proteins associated with respiration (cj0107, cj0936, cj1153, cj1490c, cj1566c, cj1567c, cj1569c, cj1571c and cj1572c), confirming that the respiration chain of C. jejuni, whilst being essential for viability, is complex and not fully understood [26]. Concerning the vitamins and cofactors, predictions by FBA are uncertain because only verified transport reactions were included in the FBA model. In addition, the range of chemicals allowed Table 2 Summary of the genome wide transposon mutagenesis for C. jejuni Transposon library Tn7 Mariner Combined Number of inserts measured 2251 7654 Number of inserts in genes 2169 7380 Percentage of inserts within genes 96.35 96.42 Number of genes with 1 or more inserts 1029 1240 Number of genes with no insert 625 414 9905 9549 96.40 1421 233 in the medium for the FBA simulation was conservative because the medium composition is not well defined. This might explain the discrepancies for the biosynthesis of biotin, folic acid and pantothenate where most of the genes associated with the pathways were predicted to be essential by FBA, but were not essential according to the transposon mutagenesis. Riboflavin was assumed to be present in the medium and used by the cell [49] so it was predicted non-essential by FBA in agreement with our transposon mutagenesis data. In the transposon study of Stahl and Stintzi [20], they proposed that ribo- flavin biosynthesis is an essential pathway, perhaps because they used a different medium. Although ubiqui- none has not been isolated from C. jejuni [34], the gen- ome is predicted to encode three proteins that participate in ubiquinone biosynthesis [23]. Cj0324 could be attributed to the synthesis of menaquinone but cj0546 (UbiD) did not have any transposon inserts