Elongation of the Transcript

Details of phosphodiester bond formation. The a, /3, and y phosphates are indicated on the initiating NTP, which in this case is ATP. The colored ovals represent NTP-binding sites on the RNA polymerase. The biochemistry of bond formation in RNA synthesis is very similar to that in DNA synthesis. 

As the polymerase traverses the DNA, it must continually cause a melting or strand separation of the DNA so that a single DNA template strand is available at the active site of the enzyme. During elongation, one base pair re-forms behind the active site for every base pair opened in front of it. The short transient RNA-DNA hybrid duplex that forms between the newly synthesized RNA and the unpaired region of the DNA helps to hold the RNA to the elongating complex. 

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Elongation of the transcript occurs by incorporation of ribonucleotides to create a copy or RNA complement of the DNA template. 

Alternative Sigma Factors Trigger Initiation of Transcription at Different Promoters Elongation of the Transcript Termination of Transcription Comparison of Escherichia coli RNA Polymerase with DNA Poll and PolIII... 

General transcription factors (GTFs) help to localize the RNA polymerase correctly on the promotor and to form a transcription-competent initiation complex. They serve to impose a specific structure on the transcription start site, and some of them are required for elongation of the transcript. 

Irinotecan is a topoisomerase-I inhibitory agent that prevents the initiation and elongation of RNA transcription, DNA replication, and supercoiling of DNA (44). Investi-... 

The large subimit of RNA polymerase II plays an important role at the beginning of the transcription process. The large subimit of the mammalian enzyme contains 52 copies of the heptamer sequence YSPTSPS in the C-terminal domain (CTD) at which phosphorylation occurs. Phosphorylation occurs extensively on the Ser-residues of the CTD, to a lesser degree at the Thr-residues, and, very rarely, at the Tyr-residues. Two forms of RNA polymerase II can be isolated from cellular extracts a underphosphory-lated form and a hyper-phosphorylated form. The isoforms fulfill different functions RNA polymerase found in the initiation complex tends to display little or no phosphorylation at the C-terminus of the large subunit, while RNA polymerase II active in elongation is hyperphosphorylated in this region of the protein. 

MECHANISM FIGURE 26-1 Transcription by RNA polymerase in E. coli. For synthesis of an RNA strand complementary to one of two DNA strands in a double helix, the DNA is transiently unwound, (a) About 17 bp are unwound at any given time. RNA polymerase and the bound transcription bubble move from left to right along the DNA as shown facilitating RNA synthesis. The DNA is unwound ahead and rewound behind as RNA is transcribed. Red arrows show the direction in which the DNA must rotate to permit this process. As the DNA is rewound, the RNA-DNA hybrid is displaced and the RNA strand extruded. The RNA polymerase is in close contact with the DNA ahead of the transcription bubble, as well as with the separated DNA strands and the RNA within and immediately behind the bubble. A channel in the protein funnels new nucleoside triphosphates (NTPs) to the polymerase active site. The polymerase footprint encompasses about 35 bp of DNA during elongation. 

To enable RNA polymerase to synthesize an RNA strand complementary to one of the DNA strands, the DNA duplex must unwind over a short distance, forming a transcription bubble. During transcription, the E. coli RNA polymerase generally keeps about 17 bp unwound. The 8 bp RNA-DNA hybrid occurs in this unwound region. Elongation of a transcript by E. coli RNA polymerase proceeds at a rate of 50 to 90 nucleotides/s. Because DNA is a helix, movement of a transcription bubble requires considerable strand rotation of the nucleic acid molecules. DNA strand rotation is restricted... 

Termination of transcription involves stopping the elongation process at a region on the DNA template that signals termination and release of the RNA product and the RNA polymerase. Most terminators are similar in that they code for a double-stranded RNA stem-and-loop structure just preceding the 3 end of the transcript (fig. 28.11). Such structures cause RNA polymerase to pause, terminate, and detach. Two types of terminators have been distinguished. The first is sufficient without any accessory factors it contains about six uridine residues following the stem and loop (see fig. 28.11). The second type of terminator lacks the polyU stretch and requires a protein factor called rho to facilitate release. 

Accordingly, some effort has been devoted to studying the effects of cisplatin on transcription. In vitro experiments with RNA polymerases demonstrated that productive elongation activity was prematurely terminated by the whole spectrum of cisplatin-DNA adducts, but not by the /ran.y-DDP 1,3-intrastrand adducts [150-152], Selective bypass of trans-DDP adducts was also demonstrated in XPA cells, suggesting that repair of the DNA lesions did not contribute to differential transcription inhibition by the platinum compounds [153], In vivo, hormone-induced chromatin remodeling and subsequent transcription from the MMTV promoter was specifically inhibited by cisplatin [154], In this case, platinum adducts seemed to cause a decrease in the DNA binding of one of the transcription factors, NF1. Several chromatin-associated proteins, such as the linker histone protein HI or... 

Phenoxazinone production was as well observed in incubation media of Secale cereale, but not in such of Vida faba and Triticum aestivum [180]. The compounds can be detected is well in incubation media of several dicotyledonous species [187]. Since surface sterilization of oat caryopses with NaOCl did not prevent phenoxazinone production, it is possible that the responsible microorganism(s) are located within the caryopses. Phenoxazinone itself has an inhibitory effect on oat radicle elongation, probably caused by intercalation of the phenoxazinone ring system to DNA, as it is known from the phenoxazinone ring system of the transcription inhibitor actinomycin D, an antibiotic produced by Strepto-myces species. 

P. H. von Hippel An integrated model of the transcription complex in elongation, termination, and editing. Science 281,660 (1998). 

DNA stores genetic information in a stable form that can be readily replicated. However, the expression of this genetic information requires its How from DNA to RNA to protein, as was introduced in Chapter 4, The present chapter deals with how RNA is synthesized and then modified to prepare for its translation into protein. We begin with transcription in prokaryotes and focus on the three stages of transcription promoter binding and initiation, elongation of the nascent RNA transcript, and termination at the end of the gene. 

Eukaryotic mRNAs contain an unusual 7-methyl guanosine at the 50 end of the transcript called a 50 cap. This guanosine is added to the transcript shortly after RNA synthesis is initiated by enzymes associated with the RNA pol II elongation complex. There is an unusual 50,50-triphosphate linkage in the 50 cap between the guanosine and the first nucleotide of the mRNA (usually adenine), as shown in Figure 25.9. 

The pathway of transcription initiation is becoming much better defined (Fig. 26-6a). It consists of two major parts, binding and initiation, each with multiple steps. First, the polymerase binds to the promoter, forming, in succession, a closed complex (in which the bound DNA is intact) and an open complex (in which the bound DNA is intact and partially unwound near the —10 sequence). Second, transcription is initiated within the complex, leading to a conformational change that converts the complex to the elongation form, followed by movement of the transcription complex away from... 

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