Consensus promoter structures

Archaebacterial RNA polymerases are very different from their eubacterial counterparts and more closely resemble eukaryotic enzymes both in their subunit complexity and in their amino acid sequences (for review, see Puehler et al., 1989). This view is also reflected in the diversity of the DNA sequences that are used by the transcription apparatus as signals for initiation of transcription, namely, the promoters. Many attempts were made to identify a consensus promoter structure (Zillig et al., 1988). However, as more genes are isolated and characterized, the picture becomes less coherent. Earlier identification of two upstream sequences, box A and box B, located around positions — 30 and + 1, respectively, gave way to two elements —DPE (distal promoter element) and PPE (proximal promoter element)—located - 38 to - 25 and — 11 to — 2, respectively (Reiter et al., 1990). The DPE encompasses the box A sequence TTTA(A or T)A, but the PPE sequence seems to depend more on an (A + T)-rich sequence rather than on a specific DNA sequence. 

Fig. 1. CAT activities in seeds of transgenic tobacco plants containing hs promoter-CAT constructs. A, Schematic structure of chimaeric genes introduced into tobacco. Details of the construction are described by Schoffl et al. (1989,1991). HSE sequences with the consensus C-GAA-TTC-G are symbolised by boxes the synthetic HSE2 is represented by two overlapping soybean HSEs. The CaMV promoter is a truncated silent version of the 35S promoter, providing only the TATA box and the transcription start site. B, CAT assays were performed as described by Schoffl et al. (1989), using 50 pg protein from seed extracts and 10 jig from leaf extracts. Dry seeds (ds) without imbibition and 20 h imbibed seeds (is), derived from the same plant, were used. Heat treatment (hs) was carried out for 2h at 40 °C prior to protein extraction. Control extracts (c) were prepared from leaves incubated at 25 °C. cm, WC-chloramphenicol acm, acetylated form of cm.

M. Tonelli, E. Ragg, A.M. Bianucci, K. Lesiak and T.L. James. Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC) a consensus sequence for promoters recognized by sigma K RNA polymerase. Biochemistry 37... 

Marsan, L. and Sagot, M. F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification../. Comput. Biol. 7, 345-362. 

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