I know that bacterial promoters have two boxes that are recognizable by sigma factor (-10 and -35) and usually transcription start site (TSS) comes around 8 nucleotides down stream -10 box. My question: is A or G nucleotide a must at the TSS? I mean must +1 nucleotide be A or G. Or that is the preferred but also T and C are possible?
Many thanks in advance.
For the housekeeping sigma factors (sigma 70 in E. coli and the mid-log sigma factor sigma A in M. tuberculosis), these proteins associate with core RNAP (forming holoRNAP) and recognize the typical -10/-35 promoter elements. For these promoters, the TSS is typically located 7bp downstream of the -10 (but this distance may change depending on the promoter structure). RNAP prefers to initiate with purine (A or G), however, the selectivity may change to a pyrimidine (U or C), depending on the promoter structure.
Please see the paper for further details about TSS selection:
https://www.cell.com/molecular-cell/pdfExtended/S1097-2765(15)00820-5
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