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Review
. 1998 Jul;180(13):3265-75.
doi: 10.1128/JB.180.13.3265-3275.1998.

Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation

R A Mooney  1 , I Artsimovitch, R Landick
Affiliations
Review

Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation

R A Mooney et al. J Bacteriol. 1998 Jul.
No abstract available

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Figures

FIG. 1
FIG. 1
The transcription cycle. Intermediates in the four phases of transcription (promoter engagement, promoter escape, RNA chain elongation, and transcript termination) are discussed in the text. Elongation is represented by growth of the RNA chain between two transcription elongation complexes. Termination and arrest are shown occurring from the paused transcription complex to reflect the likelihood that a transcriptional pause is the first step in each. However, not all paused complexes involve RNA secondary structures as depicted, especially those that lead to arrest, which likely would be blocked by an RNA hairpin that prevents reverse translocation of the RNA transcript (see the text).
FIG. 2
FIG. 2
Structure and regulatory inputs of a transcription complex.
FIG. 3
FIG. 3
Sites of regulatory inputs to RNAP large subunits. The β and β′ subunits are shown in opposite orientation to simplify depiction of known contacts to RNA and DNA. Conserved regions (A to I for β and A to H for β′) are shaded in blue (2, 45, 126). Regions that tolerate deletion of disruption are indicated by wavy lines (104, 105). Rifampin (rifampicin) and streptolydigin resistance regions, represented by orange and yellow, respectively, are based on the locations of known amino acid changes that allow growth on the antibiotics (40, 43, 102, 106). Other features shown are (i) the location of the catalytic Mg2+ ions that bind to the Asp side chains in the highly conserved sequence DFDGD at β′460–464 (27, 128); (ii) a Cys4 Zn-finger-like-motif in β′ possibly involved in forming the downstream DNA clamp (79) and in antitermination (20); and (iii) sites of contact to 3′-proximal RNA or DNA, exiting RNA or RNA hairpins, active-site bases, and the downstream DNA duplex that are described in the text (, –79, 82, 118). The pause hairpin and upstream RNA contacts are depicted in a single block because the same bases may contact the β′ or β subunit depending on whether or not a hairpin has formed (118). The active-site contact to β′-region G is indicated with a dotted line because the RNA 3′ end makes this contact only in an arrested transcription complex (69).
FIG. 4
FIG. 4
Mechanism of hairpin-dependent pausing and ρ-independent termination. The four components of the signals are color coded: magenta, pause or terminator hairpin; green, 3′-proximal RNA; purple, bases in the active site; and blue, downstream DNA duplex. The insert shows the hairpin, 3′-proximal RNA, and active-site base components of archetypical pause and termination signals (the his leader pause and the terminator found in the trp operon attenuation control region). See the text for a description of the mechanism.
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References

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    1. Artsimovitch, I., and R. Landick. Submitted for publication.
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