Fig. 3
From: Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans
Analysis of the Glass zinc fingers. Generally, Glass homologues possess a cluster of five Cys2His2 zinc fingers, each of them containing the following motif: Cys-X2,4-Cys-X12-His-X3,4,5-His. Of these, we compared the sequences of the fourth and the fifth zinc fingers, which are responsible for recognising the DNA Glass-binding motif in PRs in vivo [34,35,36,37], from the following species: Amphimedon (Porifera), Schmidtea (Platyhelminthes), Platynereis (Annelida), Aplysia (Mollusca), Caenorhabditis (Nematoda), Drosophila (Arthropoda), Strongylocentrotus (Echinodermata) and Branchiostoma (Cephalochordata). In the table, those amino acids that match the Glass consensus sequence (deduced by aligning the homologues of different species, in the first column) appear on black background. The 3D structure of the DNA-bound Cys2His2 domain has been resolved [75], and it is expected that four amino acids per zinc finger directly recognise three base pairs. These amino acids are well evolutionarily conserved across different Glass homologues and, in the sequences that we show, they are no. 10 (D), 12 (S), 13 (T), and 16 (K) in the fourth zinc finger, and no. 38 (Q), 40 (G), 41 (N), and 44 (R) in the fifth zinc finger. Other residues and neighbouring zinc fingers are also expected to contribute to the DNA-binding specificity of Glass [76]. Similarly, we aligned Glass-like proteins from vertebrates (e.g. human) and choanoflagellates (e.g. Salpingoeca) with BLAST [24] and MUSCLE [28], but they showed little similarity to the Glass consensus sequence (shown in the second column). Furthermore, a ‘DNA-binding site predictor for Cys2His2 Zinc Finger Proteins’ has been developed and is available online [32, 33]. This software predicts that, based on their amino acid sequence, all Glass homologues (in the first column) can bind to the same DNA motif: GAAGCC, which was expected from experimental works in Drosophila and Caenorhabditis [34, 35]. By contrast, it appears that the Glass-like proteins of vertebrates and choanoflagellates (in the second column) would not be able to recognise this motif. All sequences are available in the Additional file 4