We have determined the complete nucleotide sequence of a 3292 bp cloned segment derived from the 63B heat shock cytogenetic locus of D. melanogaster. Within this segment we have positioned the start of transcription and RNA splice sites of the unique gene that encodes the 83,000 d heat shock polypeptide (hsp83 gene) by SI mapping and synthesis of cDNA from restriction fragment primed mRNA. The sequence begins at a point 879 bp upstream from the transcription start and includes the 149 bp nontranslated first exon, the 1139 bp intron and extends 1125 bp into the protein coding region. These data identify a single open translation reading frame for the first 375 amino acids of the 83,000 d polypeptide, beginning with the first ATG codon located at the 3' intron-exon junction. We discuss and demonstrate the use of E. coli exonuclease III generated single-strand DNA probes as an alternative to strand separation for S1 mapping of mRNA. We also use homology search criteria based upon known protein-DNA binding sites to compare our hsp83 sequence with other sequenced Drosophila heat shock genes. These comparisons indicate that a large region of approximately 80 bp centered around the transcription initiation point of the hsp83 gene shares only a 31% homology with the corresponding region of the hsp70 gene, whereas the hsp22, 23, 26, and 27 genes share a 54% homology with hsp70 in this region. The lower homology of the hsp83 gene is consistent with the deviant nature of this heat shock gene.

Two kinds of RNA are synthesized at the 87C1 chromosomal locus ofDrosophila melanogaster in response to heat shock. One ofthese codes for the major heat shock protein, hsp7O; the other, a13 RNA, derives from tandemly repeated a( units consisting ofadjacent a and g8 DNA elements and has no identified translation product. Another DNA element, v, flanks the 5' ends of some afi units. Here we report the complete nucleotide sequence of the 617-base-pair a and the 733-base-pair y element as well as a portion of the longer (3 element. Sequence comparisons between the y element and the two hsp7O genes at 87CI reveal that the 406 base pairs of y immediately upstream from the 5' end of the ac8 unit exhibit 97.5% homology with the sequences at and upstream from the 5' end of the hap7O genes. A similar homology also exists between y and an hap7O gene present at another heat shock locus, 87A7, which contains no ci3 units. These results, in conjunction with previous observations, strongly suggest that the coordinate induction by heat shock of the hsp7O and a(3 genes is a consequence of their homologous 5' flanking sequences. We propose that this extraordinary degree of sequence conservation stems from the recent transposition of aj3 DNA to the 87C1 locus, an event that brought ag3 sequences adjacent to, and under the regulation of, the hsp7O control element.Heat shock of Drosophila melanogaster elicits a characteristic response in all tissues that results in the coordinate synthesis ofa specific set ofproteins. Concomitantly, the synthesis ofmost other cellular proteins ceases (1). The altered pattern ofprotein synthesis induced during heat shock reflects regulation at the transcriptional, translational, and RNA processing levels. The predominant heat shock protein (hsp7O) derives from a repeated gene located at the two chromosomal sites responsible for the 87A and 87C heat shock puffs (2-4). Fig. 1 shows the arrangement of the hsp7O genes at each chromosomal locus. These genes have common sequence elements within a nontranscribed region situated upstream from the mRNA coding sequences (4, 7). In this paper we shall adopt the nomenclature of Artavanis-Tsakonas et at (4)