16In Staphylococcus aureus, the capsular polysaccharide (CP) protects against 17 phagocytosis, but also hinders adherence to endothelial cells and matrix proteins. Its 18 biosynthesis is tightly controlled resulting in a heterogeneous phenotype within a 19 population and CP being mainly detectable in non-growing cells. Capsular 20 biosynthesis genes are encoded by a conserved capA-P operon whose expression is 21 driven by an upstream promoter element (P cap ) in front of capA. The organization of 22 P cap is poorly understood, as is the interplay of different regulators that influence the 23 early-Off/late-Heterogeneous cap transcription pattern. Here, we demonstrate that 24 P cap contains a main SigB-dependent promoter. The SigB consensus motif overlaps 25 with a previously described inverted repeat that is crucial for cap expression. The 26 essentiality of the inverted repeat is derived from this region acting as a SigB binding 27 site rather than as an operator site for the proposed cap activators RbsR and MsaB. 28 Furthermore, P cap contains an extensive upstream region harboring a weak SigA-29 dependent promoter and binding sites for the cap repressors SaeR, CodY and Rot.30 We show that heterogeneous CP synthesis is determined by the combination of SigB 31 activity and repressor binding to the upstream region. The direct SigB dependency 32 and the upstream repressors are also sufficient to explain the temporal gene 33 expression pattern at the transcriptional level. However, CP synthesis remains 34 growth phase-dependent even when capA transcription is rendered constitutive, 35 suggesting additional post-transcriptional regulatory circuits. Thus, the interference of 36 multiple repressors with SigB-dependent promoter activity as well as post-37 transcriptional mechanisms ensure the appropriate regulation of CP synthesis.38 39 3 Importance 40 The majority of bacterial pathogens produce an array of polysaccharides on their 41 surface which are important virulence factors and thus serve as attractive vaccine 42 candidates. However, the synthesis and assembly of these structures is highly 43 endothelial cells (21), while CP protects bacterial cells from phagocytosis (29-31), it is 87 likely that CP heterogeneity provides better adaptability of the population as a whole. 88 So far the underlying regulatory mechanisms of this particular expression pattern 89 (early-Off/late-Heterogeneous) are only partially understood.90 5In general, P cap activity correlates with CP synthesis, indicating that regulation occurs 91 predominantly at the transcriptional level (12, 22,(32)(33)(34). Yet, the data to explain the 92 molecular mechanisms of cap regulation are puzzling. The identified transcriptional 93 start site (TSS) is not preceded by a classical Sigma factor consensus sequence 94 (12); instead, several inverted and direct repeats were identified further upstream, 95 amongst which a 10 bp inverted repeat (IR) was shown to be crucial for promoter 96 activity (12). It has been proposed that this IR functions as an operat...