Termination factors

Figure 37-6. The predominant bacterial transcription termination signal contains an inverted, hyphenated repeat (the two boxed areas) followed by a stretch of AT base pairs (top figure). The inverted repeat, when transcribed into RNA, can generate the secondary structure in the RNA transcript shown at the bottom of the figure. Formation of this RNA hairpin causes RNA polymerase to pause and subsequently the p termination factor interacts with the paused polymerase and somehow induces chain termination.

PSI] is the prion of Sup35p, a translation termination factor (Ter-Avanesyan et al., 1994 Wickner, 1994). Conversion of wild-type yeast cells to the infected state results in reduction of the termination activity and, consequendy, to a nonsense suppression phenotype. This property can be used to detect [PSI] by genetic selection (Fig. 2). Sup35p is an essential gene whose knockout leads to cell death. Therefore, it appears that the [PSI] condition corresponds to only partial inactivation of Sup35p and enough of the normal protein is left to avert cell death. 

PSI] nomenclature SUP35 Wild-type gene encoding a subunit of the translation termination factor... 

NoRC Snf2h Mouse TIP5 Interacts with RNA polymerase I transcription termination factor I (TTF-1), localized to nucleoli [292] and implicated in repression of ribosomal gene transcription [293]. 

When a stop codon appears in the A site, one of several termination factors binds the site. 

Abbreviations aa-tRNA Amino-acyl tRNA eLF Eukaryotic translation initiation factor IF Prokaryotic translation initiation factor eEF Eukaryotic translation elongation factor EF Prokaryotic translation elongation factor eRF Eukaryotic translation termination factor (release factor) RF Prokaryotic translation release factor RRF Ribosome recycling factor Rps Protein of the prokaryotic small ribosomal subunit Rpl Protein of the eukaryotic large ribosomal subunit S Protein of the prokaryotic small ribosomal subunit L Protein of the prokaryotic large ribosomal subunit PTC Peptidyl transferase center RNC Ribosome-nascent chain-mRNA complex ram Ribosomal ambiguity mutation RAC Ribosome-associated complex NMD Nonsense-mediated mRNA decay... 

While readthrough is usually a detrimental process, in some cases it can help to suppress problems, e.g. arising from premature stop codons present on the DNA level. This type of readthrough, also termed nonsense suppression, leads to the generation of a fraction of the full length protein in addition to the shortened version. Omnipotent suppressors cause nonsense suppression of all three termination codons. In this process, a near cognate tRNA successfully competes with the termination factors such that amino acid incorporation rather than premature termination of translation occurs. Omnipotent suppression can be caused by mutations in various factors involved in the process of translation termination. Nonsense suppression can also result from an aa-tRNA that decodes a termination codon (suppressor tRNA) in this case only one of the termination codons is efficiently suppressed (Hawthorne and Leupold 1974 Stansfield and Tuite 1994). 

The eukaiyotic translation termination factors eRFl and eRF3... 

Accurate selection of translation termination factors to ribosomes containing a stop codon in the A-site is less well understood. A picture is only beginning to emerge as the bacterial 708 ribosome and class I release factor RF2 atomic models have recently been fitted into cryo-EM stmctures. Via multiple interactions RF2 connects the ribosomal decoding site with the PTC and functionally mimics a tRNA molecule in the A-site. In the complex RF2 is close to helices 18, 44, and 31 of the 168 rRNA, small subunit ribosomal protein 812, helices 69, 71, 89, and 92 of the 238 rRNA, the L7/L12 stalk, and protein LI 1 of the large subunit (Arkov et al. 2000 Klaholz et al. 2003 Rawat et al. 2003). The L7/L12 stalk inter-... 

Mutants in translation termination factors that affect the fidelity of translation termination... 

The effect of mutations in eRFl and eRF3 on the efficiency of translation termination in yeast has been extensively studied. A variety of mutations in both translation termination factor subunits results in a nonsense suppression phenotype (Eustice et al. 1986 Song and Liebman 1989 All-Robyn et al. 1990 Wakem and Sherman 1990 Stansfield et al. 1995a, 1997 Bertram et al. 2000 Velichutina et al. 2001 Cosson et al. 2002 Bradley et al. 2003 Chabelskaya et al. 2004 Salas-Marco and Bedwell 2004). 

As illustrated by the [PS / ] phenomenon the relative abundance of the eRFl/eRF3 complexes is an important determinant for the efficiency of translation termination. Similar effects have been obtained in depletion studies and with eRF3 and eRFl mutants that decrease their cellular concentration (Stansfield et al. 1996 Moskalenko et al. 2003 Chabelskaya et al. 2004 Salas-Marco and Bedwell 2004). Wild type yeast contains approximately 10- to 20-fold fewer termination factors compared to ribosomes (Didichenko et al. 1991 Stansfield et al. 1992). The threshold level of eRFl/eRF3 required to maintain viability is even lower. A 10-fold decrease reduces viability by only about 10% (Valouev et al. 2002) and a decrease in eRF3 of 99% does not affect viability of the cells significantly (Chabelskaya et al. 2004). As eRF3 is associated with polysomes or ribosomes, the mechanism of translation termination depends on efficient recycling (Didichenko et al. 1991 and compare below). 

Recent studies have shown that proteins interacting with the release factors can modulate the efficiency of stop codon readthrough. Physical and functional interaction with the translation termination factors was demonstrated for different components of the translational machinery. 

Aminoglycoside effects on mutants in translation termination factors and proteins interacting with the ribosome... 

Frolova L, Seit-Nebi A, Kisselev L (2002) Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRFl. RNA 8 129-136... 

Hosoda N, Kobayashi T, Uchida N, Funakoshi Y, Kikuchi Y, Hoshino S, Katada T (2003) Translation termination factor eRF3 mediates mRNA decay through the regulation of deadenylation. J Biol Chem 278 38287-38291... 

Valouev lA, Urakov VN, Kochneva-Pervukhova NV, Smirnov VN, Ter-Avanesyan MD (2004) Translation termination factors function outside of translation yeast eRFl interacts with myosin light chain, Mlclp, to effect cytokinesis. Mol Microbiol 53 687-696... 

More important at present are their r values obtained from rate data by solving the copolymerization rate equation for three unknowns, ra, rb, and the cross-termination factor, . The results are unsatisfactory consideration in our discussion of possible reasons brings out some weaknesses in the IFP estimates of termination constants. 

As in procaryotes, the elementary steps of initiation, elongation and termination can be distinguished in eucaryotic transcription. Aside from the specific RNA polymerases, transcription in eucaryotes requires the action of numerous other proteins which are collectively known as transcription factors. Transcription factors are required at the level of initiation, elongation, and termination and are accordingly known as initiation factors, elongation factors and termination factors of transcription. 

Termination factor Some regions on the DNA that signal the ter mination of transcription are recognized by the RNA polymerase itself. Others are recognized by specific termination factors, an example of which is the rho (p) factor of E. ccii. 

Rho and other termination factors. Termination proteins can also react with specific regions of DNA or of an RNA transcript to terminate transcription.183 The best known termination factor is the rho protein a hexamer of 45-kDa subunits. It interacts with transcripts at specific termination sequences, which are often C-rich, and in a process accompanied by hydrolysis of ATP causes release of both RNA and the polymerase from the DNA.192193 Additional E. coli proteins, products of genes nus A and nus G, cooperate with the rho factor at some termination sequences.194-196c The rho hexamer is a helicase that moves along the RNA transcript in the 5 —> 3 direction driven by ATP hydrolysis. If it locates an appropriate termination signal, it may utilize its helicase activity to uncoil the DNA-RNA hybrid segment within the transcription bubble (Fig. 28-4).197 198b... 

RNA interacts with specific G proteins known as initiation, elongation, and termination factors. 

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