Having coevolved with the bacterial-type RNA polymerase (PEP), many plastidial promoters contain a variant of the -35 (TTGaca) and -10 (TAtaaT) consensus sequences of typical CT70-type E. coli promoters (Reznikov et al. 1985; for reviews see Gruissem and Tonkyn 1993; Link 1994; Hess and Börner 1999; Liere and Ma-liga 2001; Weihe 2004). In fact, the E. coli RNA polymerase is able to accurately recognize plastidial c70-type promoters (e.g. Gatenby et al. 1981; Bradley and Gatenby 1985; Boyer and Mullet 1988; Eisermann et al. 1990). Since plastidial CT70-type promoters are recognized by PEP, they are also often termed PEP promoters. In addition to the core motifs, some PEP promoters contain regulatory ciselements. One of the best-characterized PEP promoters ensures transcription of the psbA gene, which encodes the D1 photosystem II reaction center polypeptide (Link 1984; Gruissem and Zurawski 1985; Boyer and Mullet 1986, 1988). In vivo psbA transcription is developmentally timed and activated by light (Klein and Mullet 1990; Schrubar et al. 1990; Baumgartner et al. 1993). In vitro characterization of the mustard psbA promoter identified a TATATA promoter element between the -10 and -35 hexamers resembling the TATA-box of nuclear genes transcribed by RNA polymerase II (Fig. 4; Eisermann et al. 1990; Link 1994). Basic transcription levels in plastidial extracts prepared from both dark and light grown plants were obtained in vitro with both the TATATA element together with the -10 region. Nonetheless, presence of the -35 element was essential for enhanced transcription rates characteristic of chloroplasts of light-grown plants (Link 1984; Eisermann et al. 1990). In barley, the psbA promoter also contains the TATA-motif between the -35/-10-elements. But, unlike in mustard, the -35 sequence is absolutely required for transcription in vitro (Kim et al. 1999b). Similarly, such TATA-box is also present in the wheat psbA promoter, but does not seem to be important. Light-independent (constitutive) transcription by PEP isolated from the leaf base (base-type PEP; young plastids) required both the -10 and -35 elements for promoter activity. However, PEP isolated from the leaf tip (tip-type PEP; mature plastids) employed only the -10 region with an additional TGn motif upstream of the -10 element (Fig. 4; extended -10 sequence; Bown et al. 1997; Satoh et al. 1999). The extended -10 sequence may be involved in promoter recognition by the tip-type PEP in mature plastids indicating that basal- and tip-type PEPs may differ by their associated transcription factors (Satoh et al. 1999). Since the mustard, barley and wheat psbA promoter sequences are highly conserved, differences in the utilization of cis-elements possibly are the result of a divergent evolution of trans-factors in these species.
Interestingly, it seems that most plastidial promoters in Chlamydomonas do not possess a valid -35 element, but rather a downstream extended -10 box (Klein et al. 1992). Furthermore, even remote sequences such as the coding regions are needed for full promoter strength of the rbcL and psbA but not psbD, atpA, and atpB genes (Blowers et al. 1990; Klein et al. 1994; Ishikura et al. 1999; Kasai et al. 2003). However, the mechanism of transcriptional enhancement by these cis-acting elements within the coding regions is not yet examined and might be unique for Chlamydomonas (Shiina et al. 1998; Kasai et al. 2003). Further regulatory sequences in addition to the core promoter regions were identified in the proximity of the psbD-psbC and rbcL promoters in higher plants (Fig. 4; see Section 4.1 for details).
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