Lack of conservation of bacterial type promoters in plastids of Streptophyta

Abstract

We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes psaA, psbA, psbB, psbE, rbcL. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, de novo emergence of the promoters, their loss together with plastome genes; functional substitution of the promoter boxes by transcription activation factor binding sites.

Figure 1

Predicted promoters upstream of genes psbA, psbB, psbE, rbcL, psaA. In the cells of first column only first occurrences of each taxon name are given. In yellow are the promoter boxes and the 5'-extension of the "-10" box. Numbers are the distance to the start codon; its location is given in the last column, prepended with "c" for complement sequences. In violet are the experimentally identified transcription initiation sites in Arabidopsis thaliana and Spinacia oleracea upstream of psbA, psbB, rbcL, psaA.

Figure 2

Nucleotide frequency distribution for the alignments shown in Fig. 1.

Figure 3

The 5'-leader regions upstream of gene psbB. In the cells of first column only first occurrences of each taxon name are given. Numbers to the left of the sequences are distances from the 5'-edge to the start codon, which location is specified in the last column ("c" stands for complement sequences). In spinach the region is located precisely between the mRNA cleavage site and the start codon. Conserved putative mRNA-protein binding sites downstream of the cleavage site are shown in green. Conserved putative ribosome binding sites close to the start codon are in yellow.