Organization and nucleotide sequence of the genes encoding the large subunits A, B and C of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius

Abstract

The genes for the three large subunits A, B and C, of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius DSM 639, were identified and characterized. The three genes follow each other immediately in the order B-A-C, which corresponds to that found in the rpoBC operon of the Escherichia coli genome. The transcription products formed in vivo were studied by Northern analysis and the start-points were determined by S1-nuclease mapping and primer directed extension analysis. The three RNA polymerase subunit genes were co-transcribed together with an open reading frame (ORF) of 88 amino acid residues length situated immediately upstream of the B gene and two ORFs of 104 and 130 amino acid residues following the C gene (together 8500 nucleotides). The following ORF, encoding a protein of 118 amino acids homologous to the ribosomal protein S12 of E. coli, was weakly transcribed with the large co-transcript and strongly from an own promoter. The derived amino acid sequence of the B-subunit was found to be homologous to the B- (second largest) subunits of the eukaryotic nuclear polymerases I, II and III and to the eubacterial beta-subunit. The combined A + C-subunits correspond to the A- (largest) subunits of the eukaryotic RNA polymerases I, II and III and to the eubacterial beta'-subunit. The amino acid sequence similarity of the Sulfolobus subunits to the eukaryotic components is clearly higher than to the E. coli subunit.