Termination, of transcription

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. 

Comparison of Escherichia coli RNA Polymerase with DNA Poll and PolIII 

In table 28.3 the bacterial RNA polymerase and the bacterial DNA polymerase are compared. Both types of enzymes are DNA-template-directed and require 4 NTPs and a divalent cation. While RNA polymerase makes single-stranded 

Sigma Factor Gone Consensus Sequence -35 Region -10 Region Genes Recognized fiWSHR 

Important features of a typical transcription unit. DNA is shown with promoter and terminator regions expanded below. RNA is transcribed starting in the promoter region at +1 and ending after the stem and loop of the terminator. The protein resulting from translation of this RNA is shown above with its N and C termini indicated. 

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Kao SY, Caiman AF, Luciw PA, Peterhn BM (1987) Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature 330(6147) 489-493... 

The 19-mer sequence must not contain four or five consecutive T or A residues, because this would act as a premature termination of transcription signal for the poly III complex. 

Eukaryotes have a specific signal for termination of transcription however, prokaryotes seem to have lost this mechanism. Once started, RNA polymerase keeps going, making a primary transcript [pre-mRNA or hnRNA (for heterogeneous nuclear)] until far past the end of the final mRNA message. 

There is a single prokaryotic RNA polymerase that synthesizes all types of RNA in the cell. The core polymerase responsible for making the RNA molecule has the subunit structure Ojpp. A protein factor called sigma (a) is required for the initiation of transcription at a promoter. Sigma factor is released immediately after initiation of transcription. Termination of transcription sometimes requires a protein called rho (p) faaor. This enzyme is inhibited by rifampin. Actinomycin D binds to the DNA preventing transcription. 

Transcription factors (such as TFIID for RNA polymerase II) help to initiate transcription. The requirements for termination of transcription in eukaryotes are not well understood. All transcription can be inhibited by actinomycin D. In addition, RNA polymerase II is inhibited by a-amanitin (a toxin from certain mushrooms). These points are summarized in Table 1-3-1,... 

Termination of transcription Stem and loop + UUUUU Stem and loop + rho factor Not well characterized... 

Premature (upstream) termination of transcription when histidine is present... 

Eukaryotic DNA contains sequences recognized as termination signals in E. coli, resulting in premature termination of transcription and a truncated protein. Also, there are differences in codon preference affecting translation, which may ultimately... 

Termination of transcription occurs when RNA pol traverses a termination signal, and this process may require the cooperation of p (rho) factor. 

Only one of the two DNA strands is transcribed into RNA and is called the sense strand. The DNA is unwound in order to make the sense strand available for base pairing. As the transcriptional complex moves along the DNA template extending the RNA chain, a region of local unwinding moves with it. Termination of transcription involves the ability of RNA polymerase II to recognize the sequences that indicate that the end of the gene has arrived and no further bases should be added to the RNA chain. 

In higher eucaryotes the 3 -end of matme mRNA is not produced as a result of termination of transcription. Rather, the 3 -end of the primary transcript is cut at a specific site and a poly-A sequence is appended. Polyadenylation precedes the splicing of the primary transcript. 

FIGURE 26-7 Model for p-independent termination of transcription in f. coli. RNA polymerase pauses at a variety of DNA sequences, some of which are terminators. One of two outcomes is then possible the polymerase bypasses the site and continues on its way, or the complex undergoes a conformational change (isomerization). In the latter case, intramolecular pairing of complementary sequences in the newly formed RNA transcript may form a hairpin that disrupts the RNA-DNA hybrid and/or the interactions between the RNA and the polymerase, resulting in isomerization. An A=U hybrid region at the 3 end of the new transcript is relatively unstable, and the RNA dissociates completely, leading to termination and dissociation of the RNA molecule. This is the usual outcome at terminators. At other pause sites, the complex may escape after the isomerization step to continue RNA synthesis. 

Rho-independent termination of transcription. A. An example of a palindrome in double-stranded DNA. B. A transcribed DNA palindrome codes for RNA that can form a hairpin turn. 

The process of RNA synthesis is called transcription. The enzyme that synthesizes RNA is RNA polymerase, which is a multisubunit enzyme. The core enzyme has four subunits—2 a, 1 p, and 1 p, and possesses 5 —>3 polymerase activity. The enzyme requires an additional subunit—sigma (a) factor—that recognizes the nucleotide sequence (promoter region) at the beginning of a length of DNA that is to be transcribed. Another protein—rho (p) factor—is required for termination of transcription of some genes. 

DNA contains numerous other protein binding sites which are not palindromes but whose sequences represent additional encoded information. The RNA transcripts likewise contain sequences that direct the catalytic machinery involved in splicing, that bind to ribosomal proteins, that control rates of transcription, and that cause termination of transcription. 

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... 

Rho factor. A protein involved in the termination of transcription of some messenger RNAs. 

K9. Kruse, B., Narasimhan, N., and Attardi, G., Termination of transcription in human mitochondria Identification and purification of a DNA binding protein factor that promotes termination. Cell 58, 391-397 (1989). 

Hough, C., Kamisue, S., Cameron, C., Notley, C., Tinlin, S., Giles, A. and Lillicrap, D. (2002). Aberrant splicing and premature termination of transcription of the FVIII gene as a cause of severe canine hemophilia A Similarities with the intron 22 inversion mutation in human hemophilia. Thromb. Haemost. 87, 659-665. 

Fig. 4. A typical hairpin structure formed by the 3 end of an RNA molecule during termination of transcription.

Termination of transcription occurs usually at a stretch of T residues preceded by a GC-rich region (Dennis, 1986). Sometimes this GC-rich region is involved in a short, inverted repeat (May et al., 1989). 

Termination of transcription in vitro is classified as to its dependence on the protein factor, rho (p). Rho-independent terminators have a characteristic structure, which features (a) A strong G-C rich stem and loop, (b) a sequence of 4-6 U residues in the RNA, which are transcribed from a corresponding stretch of As in the template. Rho-factor-depen-dent terminators are less well defined, as shown in Figure 10-8. 

Figure 8-8. The mitcochondrial tRNALeu(UUR) gene. The diagram shows the position of the A3243G mutation. The nucleotides marked with an asterisk are involved in termination of transcription.

Are termination codons associated with termination of transcription or termination of translation ... 

DNA sequence located roughly 20 bases on the 5 side of the termination site. The RNA produced on transcription of this region is able to form a hairpin structure that causes the RNA polymerase to stall and eventually dissociate from the DNA template. A stretch of uridyl nucleotides at the 3 end of the RNA hairpin is part of the rho-inde-pendent terminator sequence that is also believed to help destabilize the enzyme-DNA complex. A rho-dependent terminator also contains a self-complementary sequence capable of forming a hairpin structure. In an unknown mechanism, the rho protein hydrolyzes ATP and destabilizes the RNA polymerase-DNA complex as it stalls at the hairpin, eventually leading to the termination of transcription. 

The tasks of transcriptional and translational signal recognition involve the prediction of promoters and sites that function in the initiation and termination of transcription and translation. Bacterial promoter sites, specifically the Escherichia coli RNA polymerase promoter site, are now very well characterized. The main problem is that the two conserved regions of the bacterial promoter, the -10 and -35 regions, are separated from each other by 15 to 21 bases, making the detection of the entire promoter as a single pattern difficult. Eukaryotic promoters are less well characterized than their bacterial equivalents. The major elements are the CCAAT box, GC box, TATA box and cap site. 

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