Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum

We mapped transcription start sites for ten unrelated protein-encoding Pyro baculum aerophilum genes by primer extension and S-1 nuclease mapping. All of the mapped transcripts start at the computationally predicted translatio n start codons, two of which were supported by N-terminal protein sequencin g. A whole genome computational analysis of the regions from -50 to +50 nt around the predicted translation starts codons revealed a clear upstream pa ttern matching the consensus sequence of the archaeal TATA box located unus ually close to the translation starts. For genes with the TATA boxes that b est matched the con sensus sequence, the distance between the TATA box and the translation start codon appears to be shorter than 30 nt. Two other pro moter elements distinguished were also found unusually close to the transla tion start codons: a transcription initiator element with significant eleva tion of C and T frequencies at the -1 position and a BRE element with more frequent A bases at position -29 to -32 (counting from the translation star t site). We also show that one of the mapped genes is transcribed as the fi rst gene of an operon. For a set of genes likely to be internal in operons the upstream signal extracted by computer analysis was a Shine-Dalgarno pat tern matching the complementary sequence of P. aerophilum 16 S rRNA. Togeth er these results suggest that the translation of proteins encoded by single genes or genes that are first in operons in the hyperthermophilic crenarch aeon P. aerophilum proceeds mostly, if not exclusively, through leaderless transcripts. Internal genes in operons are likely to undergo translation vi a a mechanism that is facilitated by ribosome binding to the Shine-Dalgarno sequence. (C) 2001 Academic Press.