Organization and expression of a Thermus thermophilus arginine cluster: Presence of unidentified open reading frames and absence of a Shine-Dalgarno sequence

A group of genes regulated by arginine was found clustered in the order arg F-ORF1-argC-argJ-ORF4 between other, as yet uncharacterized, open reading f rames (ORFs). Transcription starts were identified immediately upstream fro m argF and ORF4. Arginine repressed transcription that was initiated at arg F but induced transcription of ORF4. The functions of ORF1 and ORF4 are unk nown, but analysis of the sequence of ORF4 suggests that it is a membrane p rotein, possibly involved in transport of arginine or a related metabolite. Mobility shift and DNase I footprinting have revealed specific binding of pure Escherichia coli ArgR to the promoter region of Thermus thermophilus a rgF. These results suggest that argF transcription is controlled by a repre ssor homologous to those characterized in enteric bacteria and bacilli. The rmus argF mRNA is devoid of Shine-Dalgarno (SD) sequences. However, downstr eam from the ATG start codon of argF and many other Thermus genes (with or without an SD box), sequences were found to be complementary to nucleotides 1392 to 1409 of Thermus 16S rRNA, suggesting that an mRNA-rRNA base pairin g in this region is important for correct translation initiation.