For studies of promoter regulation as mediated by metals, M. smegmatis strains were grown in Sauton medium treated with Chelex 100 resin (Sigma-Aldrich), as previously described [37]. After Chelex 100 treatment and sterilization, Sauton medium was integrated with 1 mM MgSO4 and, in some cases, with other metals, as indicated in Results. When required, streptomycin LDC000067 in vitro was added at the concentration of 10 μg/ml. Expression and purification of recombinant M. smegmatis Zur and IdeR proteins M. smegmatis zur (furB) and ideR genes were amplified by PCR with the respective primers RG329-RG330

and IdeR F- IdeR R (Table 1), and cloned into pGEX-6P-1 vector. E. coli XL1-Blue cultures, carrying the recombinant plasmid containing the ideR gene, were grown to log phase (OD600 = 0.5–0.8), induced by addition of 0.1 mM IPTG and incubated at 37°C for 3 hours. M. smegmatis Zur protein was induced by addition of 0.1 mM IPTG and incubated overnight at 26°C. Cells were subsequently harvested by centrifugation, find more washed with 1× PBS (8 g/l NaCl, 0.2 g/l KCl, 1.44 g/l Na2HPO4, 0.24 g/l KH2PO4) and stored at

-20°C. Table 1 Primer sequences Primer Sequence Purpose IdeR F IdeR R 5′TTGGATCCATGAACGATCTTGTCGATAC-3′ 5′-CGGAATTCTCAGACCTTCTCGACCTTG-3′ cloning of ideR coding Cilengitide ic50 region into pGEX-6P-1 RG329 RG330 5′-CCGGGATCCATGACGGGCGCGGT-3′ 5′-CCGGAATTCTCACGTCTGGTTCCCG-3′ cloning of zur coding region into pGEX-6P-1 Rv0282-1 Rv0282-2 5′-CGGGATCCCGCAACACCCTGGTC-3′ 5′-CGGGTACCCGCTGTCTCCTTCACC-3′ EMSA on rv0282 promoter region

mmp3 mmp7 5′-GCACGCTTGAGAGTTCC-3′ 5′-TGCCACTTTCGGGTC-3′ EMSA on mmpS5 promoter region Pr1MS F Pr1MS R 5′-CCAGTACTGACGCTGGAACGAGTG-3′ Mannose-binding protein-associated serine protease 5′-CCAAGCTTCTGACCACATCGCGG-3′ EMSA and cloning of msmeg0615 promoter region into pMYT131 Pr2MS F Pr2MS R 5′-CCAGTACTACGCTGACCGGCGAC-3′ 5′-CCAAGCTTCTCATGACTGTTTCCTTTC-3′ Cloning of msmeg0620 promoter region into pMYT131 Pr2MT F Pr2MT R 5′-CCAGTACTCAACGAGCCCGAGGCG-3′ 5′-CCAAGCTTCTCATAACATCTCTCC-3′ Cloning of rv0287(esxG) promoter region into pMYT131 RA1 RA2 5′-GACCACGCGTATCGATGTCGAC(T)16V-3′ 5′-GACCACGCGTATCGATGTCGAC-3′ 5′ RACE PCR reactions Ms0615-RT MS0615-1 Ms0615-2 5′-GTCGACGACGGCCGGGGTG-3′ 5′-CCGATCCACGCGTCGCAC-3′ 5′-GTCGTGTGCGAGATGGGTC-3′ 5′ RACE for msmeg0615 Ms0620-RT Ms0620-1 Ms0620-2 5′-GTCGAGCAGCGCATTGAC-3′ 5′-CGAGACCTCGACGAAACG-3′ 5′-GCATGCGCGGCCTGGAAG-3′ 5′ RACE for msmeg0620 Ms0615 A Ms0615 B 5′-GGCCTGACGGTCAACG-3′ 5′-ATCCACGCGTCGCACT-3′ qPCR for msmeg0615 Ms0620 E Ms0620 F 5′-CAGGCCGCGATGAGTT-3′ 5′-TCGAGCAGCGCATTGA-3′ qPCR for msmeg0620 mysA F mysA R 5′-CGTCGCCGATGGTCTG-3′ 5′-CCACGCCCGAAGAGC-3′ qPCR for M.