Читать книгу Snyder and Champness Molecular Genetics of Bacteria - Tina M. Henkin - Страница 147

In the first step (Figure 2.9), the RNA polymerase core enzyme binds to a σ factor to form the holoenzyme. The bound σ factor then directs the complex to the correct promoter in a process called promoter recognition or binding. The σ factor must be able to recognize the promoter even though the DNA in the promoter is still in a double-stranded state. Sigma factors consist of a number of domains held together by flexible linkers. Most σ factors are related to σ⁷⁰, and their domains play similar roles in recognizing their specific promoters. Figure 2.6C shows the conserved regions of the σ⁷⁰ family of sigma factors and the roles played by some of the conserved domains in promoter recognition and initiation of transcription.

One domain of the bound σ, σ₄, recognizes the –35 sequence when it is still in the double-stranded state. Another σ domain, σ₂, binds to the AT-rich –10 sequence. Some σ⁷⁰ promoters have additional sequence elements that interact with other domains of the RNA polymerase (Figures 2.6 and 2.10). The efficiency of binding of RNA polymerase to a promoter can be enhanced by sequences upstream of the promoter, called UP (for upstream) elements, to which the carboxy terminus of the α subunits, called αCTD (for α subunit carboxyl-terminal domain), can bind and help stabilize the binding of RNA polymerase to the DNA. A flexible domain that links αCTD and the amino-terminal domain of α (αNTD) allows αCTD to reach the UP element on the DNA. Also, some promoters have what is called an extended –10 sequence (TGN, located immediately upstream of the –10 sequence to give the sequence TGNTATAAT). This sequence is recognized by the σ₃ domain and is often found in promoters that lack a –35 sequence that is efficiently recognized by σ₄. The similarity of a promoter sequence to the consensus sequences for a particular σ, in combination with other elements that interact with other domains of RNA polymerase, dictates the efficiency with which a promoter is recognized by holoenzyme containing that σ.

Figure 2.7 Transcription begins at a promoter and ends at a transcription terminator. (A) The RNA polymerase core must bind σ factor to recognize a promoter. (B) Transcription begins when the strands of DNA are opened at the promoter, and the first ribonucleoside triphosphate (rNTP), usually ATP or GTP, enters the active site opposite the +1 nucleotide in the template strand. (C) As RNA polymerase moves along the DNA, polymerizing ribonucleotides into RNA (green), it forms a transcription bubble containing an RNA-DNA double-stranded hybrid, which helps to hold the RNA polymerase on the DNA. The sigma factor is released after RNA polymerase leaves the promoter, and transcription by the RNA polymerase core enzyme continues. (D) The RNA polymerase stops transcription, comes off the DNA, and releases the newly synthesized RNA at a transcription terminator.