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 (Eσ). In a consensus promoter, there are two short con served sequence elements. Approximately 35-bp upstream of the TSS there is a consensus sequence of eight nucleotide pairs (consensus: 5′-TGTTGACA-3′) to which the RNAP binds to form the so closed promoter complex. More proximal to the TSS—about 10 nucleotides upstream—is a six-nucleotide pair A+T-rich sequence (consensus: 5′-TATAAT-3′). These conserved sequence elements together comprise the promoter, and are shown schematically in Figure 1. The latter sequence has a lower melting temperature because of its lack of GC nucleotide pairs. Thus, this so-called “TATA box” is thought to ease the dissociation of the two DNA strands so that RNA polymerase bound to the promoter region can have access to the nucleotide sequence of its immediately down stream template strand. Once the process of strand separation 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 TSS, and in all cases the sequences between the two promoter elements have no similarity but still provide critical spacing functions that facilitate recognition of −35 and −10 sequences by the cognate RNA polymerase holoenzyme. Within a bacterial cell, different sets of genes are often coordinately regulated. One important way that this is accomplished is through the fact that these coregulated genes share particular −35 and −10 promoter sequences. These unique sets of promoters are recognized by different σ-factors bound to core RNA polymerase as intimated earlier (ie, Eσ1 , Eσ2 ,…).

Fig1. Prokaryotic promoters share two regions of highly conserved nucleotide sequence. These regions are located 35- and 10-bp upstream of the TSS, 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, while sequences downstream of the +1 TSS are numbered in a positive sense. Also, by convention, the promoter DNA regulatory sequence elements such as the −35 and the −10 TATAAT elements are described in the 5′→3′ direction and as being on the coding strand. These elements function only in double-stranded DNA. Other transcriptional regulatory elements, however, can often act in a direction independent fashion, and such cis-elements are drawn accordingly in any schematic. Note that the transcript produced from this transcription unit has the same polarity or “sense” (ie, 5′→3′ orientation) as the coding strand. Termination determining cis-elements reside at the end of the transcription unit (see Figure 36–6 for more detail). By convention, the sequences downstream of the site at which transcription termination occurs are termed 3′-flanking sequences.

Bacterial RNAP alone has the intrinsic ability to specifically terminate transcription on about 50% of cellular genes. On the remaining bacterial genes the accessory ρ (rho) termination factor is required. Proposed mechanisms for ρ-independent and ρ-dependent transcription termination events are presented in Figure 2. The majority of eukaryotic mRNA gene transcription events require multiple accessory transcription factors.

Fig2. Two major mechanisms of transcription termination in bacteria. (A) Bacterial RNAP can directly terminate transcription following the recognition of both specific RNA and DNA signals within transcripts/transcription units. In such situations, the transcription termination signal contains an inverted, hyphenated repeat (the two boxed areas) followed by a stretch of A nucleotides in the template strand (here, bottom strand). The inverted repeat-containing sequences, when transcribed into RNA, can generate a secondary structure like that present in the RNA transcript shown. Formation of this RNA hairpin causes RNA polymerase to pause and on recognition of the polyA sequence in the template strand induces transcription chain termination. (B) In cases where genes do not contain the two cis-elements noted earlier, a novel guanine-rich element in the DNA, and an accessory transcription factor, the ρ-protein, together serve to facilitate transcription termination. The transcript contains a run of C-residues that serve as a binding site for the ρ-factor, itself a hexameric ATPase. When present in the transcript, this element, termed the ρ-factor utilization site, or rut, is directly recognized by ρ-factor. On rut element binding, its intrinsic ATPase activity is activated and ρ-factor translocates 5’ to 3’ on the transcript until ρ encounters the transcribing RNA polymerase. ρ-factor-RNAP interaction induces transcription termination and DNA, RNA, and protein dissociation.

As discussed in detail in Chapter 38, bacterial gene transcription is controlled through the action of repressor and activator proteins. These proteins typically bind to unique and specific DNA sequences that lie adjacent to promoters. These repressors and activators affect the ability of the RNA polymerase to bind promoter DNA and/or form open complexes.

The net effect is to stimulate or inhibit PIC formation and transcription initiation—consequently blocking or enhancing specific RNA synthesis.

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مواضيع ذات صلة

Eukaryotic Promoters Are More Complex

RNA Synthesis is A Cyclical Process that Involves RNA Chain Initiation, Elongation, & Termination

RNA is Synthesized From A DNA Template by RNA Polymerases

DNA & Chromosome Integrity Is Monitored Throughout the Cell Cycle

All Organisms Contain Elaborate Evolutionarily Conserved Mechanisms to Repair Damaged DNA

Micro-RNA and Long Noncoding RNA

Histone Organization

Noncoding DNA

DNA Synthesis Occurs During the S Phase of the Cell Cycle

Formation of Replication Bubbles

Initiation & Elongation of DNA Synthesis

The Exact Function of Much of the Mammalian Genome is Not Well Understood