Reutimann I-BET-762 nmr BB1002 Newman mec, MRSA derivative, Mcr [26] BS307 BB1002 PU-H71 mouse ΔesxA, markerless deletion This study NM143 Newman GISA derivative, in vitro selected mutant; Ter [27] BS308 NM143 ΔesxA, markerless deletion This study E. coli     DH5α F-Φ80d/acZΔM15 recA1 Invitrogen Plasmids     pKOR1 E. coli-S. aureus shuttle vector for markerless deletions

using the counter selection system [28] pAC7 Expression plasmid containing the PBAD promoter and the araC gene; Cmr [29] pAC7-sigB pAC7 with a 0.75 kb fragment containing the gene sigB from S. aureus Col; Cmr [30] pBus1 E. coli-S. aureus shuttle plasmid with multicloning site from pBluescript II SK (Stratagene) and the rrnT14 terminator sequence from pLL2443; Tcr [31] pyabJ pBus1

containing a bacA AZD9291 supplier promoter-yabJ ORF fusion construct; Tcr [10] pspoVG pBus1 containing a bacA promoter-spoVG ORF fusion construct; Tcr [10] pyabJspoVG pBus1 containing a bacA promoter-yabJ-spoVG operon fusion construct; Tcr [10] pSP-luc + Firefly luciferase casette vector; Apr Promega pesxAp-luc + pBus1 containing an esxAp-luc + fusion fragment; Tcr This study pesxApΔσA -luc + pesxAp-luc + with deletion of the σA promoter This study pesxApΔσB -luc + pesxAp-luc + with deletion of the σB promoter This study pSB40N Promoter probe plasmid; Apr [29] pasp23p pSB40N with a 0.6 kb fragment covering the asp23 promoter region fused to the reporter gene lacZα; Apr [30] pesxAp pSB40N with a 0.5 kb fragment covering the esxA promoter region fused to the reporter gene lacZα; Apr This study pyabJp pSB40N with a 0.4 kb fragment covering the yabJ promoter region fused to the reporter gene lacZα; Apr This study pSTM07 pSB40N with a 0.37 kb fragment covering the capA promoter region fused to the reporter gene lacZα; Apr [9] a Abbreviations are as follows: Apr, ampicillin resistant; Cmr, chloramphenicol

resistant; Emr, erythromycin Carnitine dehydrogenase resistant; Mcr, methicillin resistant; Tcr, tetracycline resistant; Ter, teicoplanin resistant. Molecular biological methods General molecular biology techniques were performed according to standard protocols [32, 33]. Sequencing was done using the Big Dye Terminator Cycle Sequencing Ready Reaction Kit and an ABI Prism 310 genetic analyzer (Applied Biosystems, Foster City, CA, USA). Sequences were analyzed with the Lasergene software package (DNASTAR, Inc., Madison, WI, USA). Construction of ΔesxA mutants The markerless deletion of esxA (nwmn_0219) in strains Newman, BB1002 and NM143 was constructed using the counter selection system of pKOR1 as described by Bae et al. [28], using primer pairs oBS43/oBS44 and oBS45/oBS46 (Table 2) to amplify sequences framing esxA. Correct deletion of esxA in BS304, BS307 and BS308, respectively, was confirmed by sequencing and Southern blot analysis, and the absence of major rearrangements by pulsed-field gel electrophoresis [34].