Taken together, the literature suggests that MAP strains vary in their iron dependent gene regulation. To test this further, we profiled their transcriptomes and proteomes in response to iron and demonstrated that iron induced metabolic pathways are significantly diverse. Methods Bacterial strains, DNA manipulations and media Mycobacterium avium subsp. paratuberculosis strains MAP1018 (C MAP) and MAP7565 (S MAP) were grown in Middlebrook 7H9 supplemented with OADC enrichment medium and mycobactin J (2 mg/mL; Allied Monitor, Fayette, MO). To test the Tipifarnib cell line hypothesis that gene regulation may be dependent on iron availability MAP strains were grown in Middlebrook 7H9 medium

without mycobactin J or Sauton medium (0.5 g KH2PO4, 0.5 g MgSO4, 4.0 g L-asparagine, 60 ml glycerol, 0.05 g ferric ammonium citrate, 2.0 g citric acid, 0.1 ml 1% (w/v) ZnSO4 and 2.5 ml 20% Tween 80 in 1 liter). Growth of MAP strains in the absence of mycobactin J took over PLX4032 mw 6 months to provide sufficient material for proteomics and transcriptional profiling. For iron restriction, 2,2′-dipyridyl (Sigma Aldrich, St. Louis, MO) was added at a concentration of 200 μM. MAP7565 and MAP1018 have been genotyped by SSR as well as comparative genomics using oligoarrays. They represent the typical genomotypes of sheep and cattle strains, respectively [18] and show distinct phenotypes in both

human and bovine macrophages [24, 25]. M. smegmatis (mc2155) and E. coli TOP10F (Invitrogen Corporation, Carlsbad, CA) competent cells were grown in Luria Bertani (LB) medium and this website antibiotics (kanamycin (20 μg/ml) or hygromycin (100 μg/ml)) were added when necessary. The open reading frames of

ideR (MAP2827) derived from C or S MAP strains were cloned into pSM417 and M. smegmatisΔideR (SM3) was complemented as previously reported [4]. Briefly, MAP2827 from MAP1018 (cideR) or MAP 7565 (sideR) was amplified via PCR using primers that carried restriction sites for BamHI and HindIII. Amplified products were double digested with BamHI and HindIII and ligated into a pre digested (BamHI and HindIII) expression plasmid pSM417. Accuracy of the ligation and orientation of MAP2827 in pSM417 was verified by sequencing. SM3 was transformed 4-Aminobutyrate aminotransferase with pSM417 carrying MAP2827 from C or S MAP strains. A seed stock from logarithmically grown (OD600 = 1.0) cultures were diluted to fresh medium to yield an OD600 = 0.1. These were grown in various aliquots under constant shaking (120 rpm) at 37°C. These cultures were monitored for their growth at weekly intervals by measuring their absorbance at 600 nm wave length using SpectraMax M2 (Molecular Devices, Sunnyvale, CA) until they reached an absorbance of 1.0 (Additional file 1, Figure S1). At this point, the cultures were then pelleted, washed in ice cold 1XPBS and re-suspended in fresh culture medium (with or without the addition of 2,2′-dipyridyl (Sigma Aldrich, St. Louis, MO)).