Organization of genes for transcription and translation in the rif region of the Escherichia coli chromosome

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Abstract
The .lambda.rifd18 transducing phage is known to carry several genes for components of transcriptional and translational machineries; these genes are clustered in the rif region at 88 min on the E. coli genetic map. They include a set of genes for rRNA (rrnB), a gene for spacer tRNA, tRNA2Glu (tgtB), 1 of the 2 genes for EF[elongation factor]-Tu (tufB), genes for 4 ribosomal proteins (rplK, A, J and L), genes for the .beta. and .beta.'' subunits of RNA polymerase (rpoB and rpoC), and genes for 3 tRNA (tyrU, gluT and thrT). An additional tRNA gene (subsequently identified as thrU by others) and a gene for a protein (protein U) with unknown functions were carried by .lambda.rifd18. The organization of these genes were analyzed by using various deletion and hybrid phages derived from .lambda.rifd18 and .lambda.rifd12, a phage related to .lambda.rif18. The expression of various genes was examined in UV-irradiated cells infected with these transducing phages. Two main conclusions were obtained. First, the 4 tRNA genes are not cotranscribed with the genes in rrnB even though these tRNA genes are located close to the distal end of rrnB. Second, the 4 ribosomal protein genes are organized into 2 separate transcriptional units; rplK and A are in one unit and rplJ and L are in the 2nd unit. The 1st group of genes had a promoter separate from that for tufB or protein U. The 2nd group of genes shares the promoter with rpoB and C. These and other results showed that the genes are organized in the following order: promoter, genes in rrnB; promoter, thrU, tyrU, (promoter?) glyT, thrT; (promoter?) tufB; promoter, a gene for protein U; promoter, rplK, rplA; promoter, rplJ, rplL, rpoB, rpoC.