Antiterminator mechanisms

Transcription of the HIV genome by RNA polymerase II Is regulated by an antitermination mechanism that requires cooperative binding by the virus-encoded Tat protein and cyclln T to the TAR sequence near the 5 end of the HIV RNA. 

Represslble Biosynthetic Systems. In enteric bacteria the represslble systems for histidine and tryptophan biosynthesis provide examples of systems controlled by positive and negative elements, respectively (see Table IV). Since the level of histidine In the colon Is among the lowest of all amino acids, expression of the histidine biosynthetic operon In the bacterium will be In hl demand (Table III). Thus, demand theory predicts that the histidine biosynthetic operon will be positively regulated (Table II). In fact, there Is good evidence to show that this operon Is controlled primarily by an antiterminator mechanism (, ). On the other hand, the level of tryptophan In the colon Is among the hipest of the amino acids and, therefore, expressl( i of the tryptophan biosynthetic operon In the bacterium... 

Figure 1 Generalized model for sensing regulatory effectors by nascent mRNA leader transcripts. Transcription attenuation mechanisms have been identified in which the nascent transcript interacts with a translating 70S ribosome, a protein, an RNA molecule or a small metabolite, (a) Binding of the effector molecule promotes transcription termination, (b) Binding of the effector molecule promotes transcription readthrough (antitermination). See text for details.

TrpR, which is a DNA binding repressor protein, regulates transcription initiation of the E. coli trpEDCBA operon. Under tryptophan limiting conditions, TrpR represses transcription initiation, whereas repression is relieved in the presence of excess tryptophan. Once transcription initiates the elongating transcription complex is subject to control by transcription attenuation (reviewed in References 5 and 6). The leader transcript can form three RNA secondary structures that are referred to as the pause hairpin, the antiterminator structure, and an intrinsic terminator hairpin. Because the antiterminator shares nucleotides in common with the terminator, their formation is mutually exclusive. The pause hairpin has two additional roles in this transcription attenuation mechanism it serves as an anti-antiterminator stmc-ture that prevents antiterminator formation, and it codes for a leader peptide. A model of the E. coli trp operon transcription attenuation mechanism is presented in Fig. 2a. 

In several bacterial species, uncharged tRNA serves as the effector molecule in controlling expression of several aminoacyl-tRNA synthetase genes and a few amino acid biosynthetic oper-ons by a conunon mechanism termed T-box antitermination. 

The most recently identified class of transcription attenuation mechanism involves direct sensing of the effector molecule by the nascent transcript (52-54). These RNA sensors control metabolically diverse pathways. As for the other attenuation and antitermination mechaiusms discussed thus far, recognition of the particular effector molecule occurs with the appropriate affinity and high specificity required for precise control of gene expression. 

This excellent review article summarizes the mechanisms responsible for processive antitermination in lambdoid bacteriophages, which includes the classic N-mediated antitermination of lambda and factor-independent antitermination of the related HK022 phage. This work was not included in this article because of space considerations. 

W. S. Yarnell and J. W. Roberts Mechanism of intrinsic transcription termination and antitermination. Science 284, 611 (1999). 

The answer is d. (Murray, pp 435-451. Scriver, pp 3-45. Sack, pp 1—40. Wilson, pp 101—120.) Bacterial DNA contains stop signals, some of which require p protein. This has been demonstrated by examining the synthesis of mRNA in the presence and absence of p protein. In the absence of p protein, longer RNA molecules are often synthesized. This would seem to indicate that mRNA length can be controlled by the cell. In addition, antiterminator proteins are needed to allow certain genes to be properly expressed. Mammalian mechanisms for transcription termination, and the likely presence of factors regulating termination, are not yet characterized. 

FIGURE 11.16 The attenuation mechanism in the trp operon. The pause structure forms when the ribosome passes over the Trp codons quickly when tryptophan levels are high. This causes premature abortion of the transcript as the terminator loop is allowed to form. When tryptophan is low, the ribosome stalls at the Trp codons, allowing the antiterminator loop to form, and transcription continues. 

Transcription attenuation can also occur by other mechanisms, involving RNA-binding proteins in particular. For instance, the attenuation of the trp operon in B. subtilis is mediated by TRAP (for trp RNA-binding attenuation protein, a toroid-shaped molecule) which acts by binding to the (GAJ) AG-repeat segment of the nascent transcript (92). The binding prevents formation of an antiterminator structure, and allows terminator formation and transcription termination. The active conformation of TRAP is induced by Trp binding, which renders the attenuation mechanism responsive to the availability of the product amino acid. 

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