Table 1.
List of DNA sequences of named oligonucleotides used in the present study.
Fig 1.
Pigmented antibiotic and Calcium Dependent Antibiotic phenotypes of strains used in the study.
MS agar (A), ONA (B) and R5 (C) plates illustrating the ACT and RED phenotypes and CDA bioassay plates, plus Ca2+ (D) and minus Ca2+ (E) illustrating the CDA production phenotypes of: (a) MT1110; (b) MT1110 ΔabsA2 (pMT3226); (c) MT1110 ΔabsA2 (pMT3226::3xFabsA2); (d) MT1110 Δcda.
Fig 2.
In vivo genomic distribution of 3xFAbsA2 in the region of glmT (SCO3215) and parallel measurement of adjacent gene expression.
The right hand y axis represents transcriptomic data (average log2 [cDNA/gDNA]) for MT1110 ΔabsA2 (pMT3226) (orange line) and MT1110 ΔabsA2 (pMT3226::3xFabsA2) (blue line). The left hand y axis represents chIP data (average log2 [complemented mutant/non-complemented mutant enrichment signal]) [i.e. the Cy-dye balanced average MT1110 ΔabsA2 (pMT3226::3xFabsA) enrichment ratio relative to the same probe signal from the same chromatin subjected to a mock no-Ab IP divided by the Cy-dye balanced average MT1110 ΔabsA2 (pMT3226) enrichment ratio relative to the same probe signal from the same chromatin subjected to a mock no-Ab IP] (plotted as black columns). The x axis represents the genomic position of the microarray probes and the arrows above represent genes and direction of transcription, with the main gene of interest being highlighted in red. Panels (A), (B) & (C) refer to the 14 h (mid exponential phase), 18 h (late exponential phase) and 35 h (stationary phase) time-points respectively.
Fig 3.
In vivo genomic distribution of 3xFAbsA2 in the region of cdaPSI (SCO3230) and parallel measurement of adjacent gene expression.
See legend to Fig 2 for an explanation of the axes and colour coding. Panels (A), (B) & (C) refer to the 14 h, 18 h and 35 h time-points, respectively.
Fig 4.
In vivo genomic distribution of 3xFAbsA2 in the region of cdaR (SCO3217) and parallel measurement of adjacent gene expression.
See legend to Fig 2 for an explanation of the axes and colour coding. Panels (A), (B) & (C) refer to the 14 h, 18 h and 35 h time-points respectively.
Fig 5.
In vivo genomic distribution of 3xFAbsA2 in the region of absA2 (SCO3226) and parallel measurement of adjacent gene expression.
See legend to Fig 2 for an explanation of the axes and colour coding. The biphasic 3xFAbsA2 chIP peak is indicated by the pink dotted line. Panels (A) & (B) refer to the 14 h and 18 h time-points, respectively.
Fig 6.
In vivo genomic distribution of 3xFAbsA2 in the region of redZ (SCO5881) and parallel measurement of adjacent gene expression.
See legend to Fig 2 for an explanation of the axes and colour coding. The biphasic 3xFAbsA2 chIP peak is indicated by the pink dotted line. Panels (A), (B) & (C) refer to the 14 h, 18 h and 35 h time-points, respectively.
Fig 7.
In vivo genomic distribution of 3xFAbsA2 in the region of actII orfIV (SCO5085) and parallel measurement of adjacent gene expression.
See legend to Fig 2 for an explanation of the axes and colour coding. The biphasic 3xFAbsA2 chIP peak is indicated by the pink dotted line. Panels (A), (B) & (C) refer to the 14 h, 18 h and 35 h time-points, respectively.
Fig 8.
Summary of main findings from chIP analysis of AbsA2 binding.
Schematic diagram illustrating the in vivo pattern of binding of 3xFabsA2 to selected genes from antibiotic biosynthetic gene clusters known, or predicted, to be bound by AbsA2. References providing evidence of AbsA2 binding are indicated alongside those chIP peaks they provide supporting evidence for. ‘Biphasic’ chIP peaks are shown in purple whilst ‘monophasic’ chIP peaks are shown in blue.