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Review
. 2011 Apr;14(2):142-7.
doi: 10.1016/j.mib.2011.01.012. Epub 2011 Feb 19.

Regulation of gene expression by reiterative transcription

Charles L Turnbough Jr  1
Affiliations
Review

Regulation of gene expression by reiterative transcription

Charles L Turnbough Jr. Curr Opin Microbiol. 2011 Apr.

Abstract

Gene regulation involves many different types of transcription control mechanisms, including mechanisms based on reiterative transcription in which nucleotides are repetitively added to the 3' end of a nascent transcript due to upstream transcript slippage. In these mechanisms, reiterative transcription is typically modulated by interactions between RNA polymerase and its nucleoside triphosphate substrates without the involvement of regulatory proteins. This review describes the current state of knowledge of gene regulation involving reiterative transcription. It focuses on the methods by which reiterative transcription is controlled and emphasizes the different fates of transcripts produced by this reaction. The review also includes a discussion of possible new and fundamentally different mechanisms of gene regulation that rely on conditional reiterative transcription.

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Figures

Figure 1
Figure 1
Direct control of reiterative transcription by competing NTP substrates. In this example, which uses the DNA sequence of the E. coli pyrBI initially transcribed region, the competing substrates are GTP and UTP. After synthesis of the AAUUU transcript, it can reversibly slip one base upstream due to a weak RNA-DNA hybrid. Addition of the template-encoded G residue at position +6 of the completely aligned AAUUU transcript results in an RNA-DNA hybrid that is stable enough to prevent further transcript slippage, allowing the AAUUUG transcript to be extended into full-length transcripts. Conversely, addition of a U residue at position +6 of the slipped transcript prevents addition of a G residue and entry into the productive mode of transcription through a mechanism that remains obscure. Subsequently, the AAUUUU transcript is either released from the transcription initiation complex or it slips upstream, allowing addition of another extra U residue. This process can be repeated many times, with each AAUUUUn transcript eventually released from the transcription complex.
Figure 2
Figure 2
Alternative fates of transcripts synthesized from a promoter at which conditional reiterative transcription occurs. This example compares transcripts initiated at the pyrG promoter of B. subtilis. Under certain conditions, pyrG transcripts are subject to reiterative transcription that adds up to nine extra G residues following the run of three normally templated G residues at the 5′ end of the transcript. Transcripts containing extra G residues can be extended downstream following a switch from reiterative to normally templated transcription. On the left of the figure is the sequence of a transcript that does not contain extra G residues. This transcript contains a G+C-rich (terminator) hairpin immediately followed by a U-rich tract in the pyrG leader region. These RNA elements cause intrinsic transcription termination that precludes transcription of the downstream gene. On the right of the figure is the sequence of a transcript containing six extra G residues. This transcript forms an antiterminator hairpin that includes the run of nine G residues at the 5′ end of the transcript and the upstream segment of the terminator hairpin containing a run of nine C and U residues, both of which base pair with G in RNA. The antiterminator hairpin prevents terminator hairpin formation, allowing transcription of the downstream gene.
Figure 3
Figure 3
Indirect control of reiterative transcription. In this example, which uses the E. coli codBA promoter region, indirect control of reiterative transcription occurs through transcription start site switching. Under conditions of pyrimidine excess, codBA transcription initiation occurs predominantly at position A8 (counting downstream from the −10 region). Transcripts initiated at position A8 always engage in reiterative transcription, generating only nonproductive AUUUUn transcripts that are released from the transcription initiation complex. Under conditions of pyrimidine limitation, however, the major codBA transcription start site is position G7. For the most part, G7-initiated transcripts do not engage in reiterative transcription and are normally elongated to produce full-length codBA transcripts. G7-initiated transcripts avoid reiterative transcription because they form an RNA-DNA hybrid starting with a dC:rG base pair that is stable enough to prevent transcript slippage. Thus, in the case of the codBA operon, reiterative transcription is controlled by the selection of alternative transcription start sites that occurs prior to the possibility of repetitive nucleotide addition.
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References

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