Bacterial Promoters Are Relatively Simple

Bacterial promoters are approximately 40 nucleotides (40 bp or four turns of the DNA double helix) in length, a region small enough to be covered by an E coli RNA holopolymerase molecule. In this consensus promoter region are two short, conserved sequence elements. Approximately 35 bp upstream of the transcrip tion start site there is a consensus sequence of eight nu-cleotide pairs (5'-TGTTGACA-3') to which the RNAP binds to form the so-called closed complex. More proximal to the transcription start site—about ten nu-cleotides upstream—is a six-nucleotide-pair A+T-rich sequence (5'-TATAAT-3'). These conserved sequence elements comprising the promoter are shown schematically in Figure 37-5. The latter sequence has a low melting temperature because of its deficiency of GC nucleotide pairs. Thus, the TATA box is thought to ease the dissociation between the two DNA strands so that RNA polymerase bound to the promoter region can have access to the nucleotide sequence of its immediately downstream template strand. Once this process occurs, the combination of RNA polymerase plus promoter is called the open complex. Other bacteria have slightly different consensus sequences in their promoters, but all generally have two components to the promoter; these tend to be in the same position relative to the transcription start site, and in all cases the sequences between the boxes have no similarity but still provide critical spacing functions facilitating recognition of -35 and -10 sequence by RNA polymerase holoenzyme. Within a bacterial cell, different sets of genes are often

-TRANSCRIPTION UNIT

Coding strand 5' Template strand 3'

Promoter->+<-Transcribed region

Transcription start site +1

Promoter->+<-Transcribed region

Transcription start site +1

Coding strand 5' Template strand 3'

Termination signals

-35 region

5' Flanking sequences

Figure 37-5. Bacterial promoters, such as that from Ecoli shown here, share two regions of highly conserved nucleotide sequence. These regions are located 35 and 10 bp upstream (in the 5' direction of the coding strand) from the start site of transcription, which is indicated as +1. By convention, all nucleotides upstream of the transcription initiation site (at +1) are numbered in a negative sense and are referred to as 5'-flanking sequences. Also by convention, the DNA regulatory sequence elements (TATA box, etc) are described in the 5' to 3' direction and as being on the coding strand. These elements function only in double-stranded DNA, however. Note that the transcript produced from this transcription unit has the same polarity or "sense" (ie, 5' to 3' orientation) as the coding strand. Termination ciselements reside at the end of the transcription unit (see Figure 37-6 for more detail). By convention the sequences downstream of the site at which transcription termination occurs are termed 3'-flanking sequences.

-35 region

Termination signals

"DNA

5' Flanking sequences

3' Flanking sequences

Figure 37-5. Bacterial promoters, such as that from Ecoli shown here, share two regions of highly conserved nucleotide sequence. These regions are located 35 and 10 bp upstream (in the 5' direction of the coding strand) from the start site of transcription, which is indicated as +1. By convention, all nucleotides upstream of the transcription initiation site (at +1) are numbered in a negative sense and are referred to as 5'-flanking sequences. Also by convention, the DNA regulatory sequence elements (TATA box, etc) are described in the 5' to 3' direction and as being on the coding strand. These elements function only in double-stranded DNA, however. Note that the transcript produced from this transcription unit has the same polarity or "sense" (ie, 5' to 3' orientation) as the coding strand. Termination ciselements reside at the end of the transcription unit (see Figure 37-6 for more detail). By convention the sequences downstream of the site at which transcription termination occurs are termed 3'-flanking sequences.

coordinately regulated. One important way that this is accomplished is through the fact that these co-regulated genes share unique -35 and -10 promoter sequences. These unique promoters are recognized by different O factors bound to core RNA polymerase.

Rho-dependent transcription termination signals in E coli also appear to have a distinct consensus sequence, as shown in Figure 37-6. The conserved consensus sequence, which is about 40 nucleotide pairs in length, can be seen to contain a hyphenated or interrupted inverted repeat followed by a series of AT base pairs. As transcription proceeds through the hyphenated, inverted repeat, the generated transcript can form the intramolecular hairpin structure, also depicted in Figure 37-6.

Transcription continues into the AT region, and with the aid of the p termination protein the RNA polymerase stops, dissociates from the DNA template, and releases the nascent transcript.

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