Transcript Elongation and Termination in Bacteria


Ribonucleic acid (RNA) molecules are elongated by the addition of nucleotides to the 3′ end of a nascent RNA by action of RNA polymerase. The substrates are the four ribonucleoside triphosphates. The order of their addition is directed by pairing with an unwound part of the template deoxyribonucleic acid (DNA) strand and is driven by the release of two of the phosphates as pyrophosphate. The rate of addition varies considerably from one nucleotide to the next, but the overall rate is ∼48 nt s−1 along genes encoding proteins, synchronised with the rate of translation. The elongation complex is very stable over most sequences. Termination of transcription can occur at an ‘intrinsic’ terminator – a set of sequences where the complex becomes unstable, or at a Rho‐dependent terminator, where the protein Rho acts on the RNA in the transcription complex to mediate its release. The regulation of expression of genes is controlled in many instances by the action of regulatory terminators (attenuators) or by the function of factors that affect the elongation rate and the action of terminators.

Key Concepts:

  • RNA polymerase unwinds ∼15 bp of DNA so that one strand can serve as a template for the assembly of an RNA transcript.

  • The elongation complex of RNA polymerase, DNA and nascent RNA is very stable over most DNA sequences, allowing the synthesis of transcripts that are thousands of nucleotides long.

  • Transcripts encoding protein are elongated with an average rate of 48 nt s−1, which is synchronous with the rate of translation.

  • The rate of step‐wise addition of nucleotides to the nascent RNA varies considerably from position to position on the DNA.

  • Pauses in the elongation process serves as regulatory points.

  • At the sequences of an intrinsic terminator the elongation complex becomes unstable allowing spontaneous release of a transcript.

  • Termination of transcription is mediated in some cases by action of a factor called Rho, which functions by first binding to an exposed transcript followed by acting on the RNA in a reaction powered by ATP hydrolysis.

Keywords: transcription; promoter; terminator; attenuator; ribosome; RNA polymerase; bacteriophage; Rho factor; NusA; NusG

Figure 1.

Mechanism for nucleotide addition reaction.

Figure 2.

An electron micrograph of a segment of E. coli DNA. This image shows ribosomes on RNA fibres emanating from RNA polymerase molecules on a DNA fibre. Courtesy of Dr Barbara Hamakalo, University of California at Irvine.

Figure 3.

(a) Structural model of a transcript elongation complex of a bacterial RNA polymerase (Thermus thermophilus) showing several features of the polymerase with its interactions with DNA and RNA. This image is reproduced from Nudler E (2009) Annual Review of Biochemistry 78: 335–361 with permission from the copyright holder. (b) A schematic of the elongation complex (rotated with respect to model shown in (a) to have the RNA exit site facing down). The arrows show the direction of movement of DNA into the complex. The template strand is in green, the nontemplate strand is in purple and the RNA transcript is in brown. Parts of β and β′ have been cut away to show the paths of the DNA strand. The two α subunits are at the back in this view.

Figure 4.

A model of the transcript elongation complex showing the formation of the hairpin in the transcript as it emerges from the exit site. Note that the RNA (brown) has lost some of its pairing with the template and is thus just about to be released from the complex.

Figure 5.

Rho acting to pull a nascent transcript from its attachments in the elongation complex. The 5′ segment of the RNA (brown line) is shown wrapped in a binding site in a cup at one end of the mushroom‐shaped Rho structure (shown in orange). Note that the RNA has lost some of its pairing with the template and is thus just about to be pulled away by Rho.


Further Reading

Cardinale CJ, Washburn RS, Tadigotla VR et al. (2008) Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 320: 935–938.

Epshtein V, Dutta D, Wade J and Nudler E (2010) An allosteric mechanism of Rho‐dependent transcription termination. Nature 463: 245–249.

Landick R (2006) The regulatory roles and mechanism of transcriptional pausing. Biochemical Society Transactions 34: 1062–1066.

Nudler E (2009) RNA polymerase active center: the molecular engine of transcription. Annual Review of Biochemistry 78: 335–361.

Roberts JW (2010) Syntheses that stay together. Science 328: 436–437.

Roberts JW, Shankar S and Filter JJ (2008) RNA polymerase elongation factors. Annual Review of Microbiology 62: 211–233.

Thomsen ND and Berger JM (2009) Running in reverse: the structural basis for translocational polarity in hexameric helicases. Cell 139: 523–534.

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Richardson, John P(Nov 2010) Transcript Elongation and Termination in Bacteria. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000858.pub2]