Sequence and structure conservation in yolk proteins and their genes

The yp1 and yp2 genes of Drosophila code for egg yolk proteins. Their transcription is hormone-dependent and co-ordinate. In this paper we describe the complete nucleotide sequence of the yp2 gene and of the region between these two divergently transcribed genes. We also map the mature messenger RNA on the yp2 gene sequence. We then use this information and similar information previously determined for the yp1 gene to find features common to the two genes and to the two proteins. Most features common to the nucleotide sequences flanking the two genes are consensus sequences that have been found in many other eukaryotic genes. An unusual feature common to the two genes is a potential stem-and-loop structure, which has a TATA box a capping site, ribosomal RNA homology and then a translation initiation codon at the four successive junctions between single strands and duplexes. A second unusual common feature is a 13-nucleotide sequence that is similar to a recently proposed consensus sequence for the progesterone-receptor binding site. We speculate that the stem-and-loop structure and the conserved 13-nucleotide sequence may be involved in the co-ordinate, hormone-dependent expression of the genes. In examining features common to the two proteins we find that the sequences are 53% homologous and the predicted secondary structures are nearly identical. We propose that the conserved secondary structure is important to the oligomerization and perhaps to other activities common to these proteins.