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Review
. 2000 Aug;182(15):4129-36.
doi: 10.1128/JB.182.15.4129-4136.2000.

The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor

M Buck  1 , M T Gallegos, D J Studholme, Y Guo, J D Gralla
Affiliations
Review

The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor

M Buck et al. J Bacteriol. 2000 Aug.
No abstract available

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Figures

FIG. 1
FIG. 1
RNA polymerase holoenzyme containing ς54 binds to −24 and −12 consensus promoters to form a stable closed complex which is transcriptionally silent. This complex can be disrupted by heparin in vitro. Activator-mediated nucleotide hydrolysis drives full open promoter complex formation. Open complexes are insensitive to heparin in vitro. NTP, nucleoside triphosphate; NDP, nucleoside diphosphate.
FIG. 2
FIG. 2
Domain organization of the ς54 protein. E. coli ς54 (amino acids 1 to 477) can be divided into three regions (I to III [80]). DNA-binding functions (127) and associated motifs (DNA cross-linking [XLINK] region [7], helix-turn-helix [HTH] motif [81], and RpoN box [111]) reside in the C terminus, adjacent to sequences that modulate DNA binding (amino acids 180 to 306) (12). Activator responsiveness involves region I sequences (10, 98, 109), and region II is acid and variable. The main core binding determinant from amino acids 120 to 215 (40, 127) is shown. A full ς54 amino acid alignment of known sequences is available at http://www.bio.ic.ac.uk/staff/mbuck/alignment.rtf.
FIG. 3
FIG. 3
Cartoon model showing activities proposed for activation via DNA melting. Dark shading indicates activities primarily in ς54. These activities include duplex (double-stranded DNA) binding at nucleotides −24 and −12 and fork junction binding. The −7 to −11 single-strand binding activity is seen only after activation. Light shading indicates single-strand binding activities contributed by RNA polymerase holoenzyme. The solid circle represents the −11 connector nucleotide that inhibits the spread of unactivated melting when unpaired. (Top) Prior to activation, the holoenzyme is stabilized on the DNA using primary interactions at nucleotide −24. The unactivated complex includes a form shown here in which a molecular structure near −12 contributes to binding and prevents the spread of early DNA melting to downstream positions. The N terminus and the fork junction connector position −11 (solid circle) are key determinants in locking the system in a closed state. Deregulated bypass mutations destroy this ς54-DNA structure at −11 and allow partial engagement of the downstream single-strand binding activities; these are shown downstream of −12 and above and below the DNA in an unengaged state. (Bottom) Upon activation, ATP triggers conformational changes in ς54 at the fork junction that involve the ς54 N terminus. The upstream nontemplate strand binding activity is exposed, and interactions through the connector can now be established. The single-strand DNA-binding activities stabilize the spread of melting.
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References

    1. Barrios H, Valderrama B, Morett E. Compilation and analysis of ς54-dependent promoter sequences. Nucleic Acids Res. 1999;27:4305–4313. - PMC - PubMed
    1. Bertoni G, Fujita N, Ishihama A, de Lorenzo V. Active recruitment of ς54 RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and αCTD. EMBO J. 1998;17:5120–5128. - PMC - PubMed
    1. Brun Y V, Shapiro L. A temporally controlled sigma-factor is required for polar morphogenesis and normal cell division in Caulobacter. Genes Dev. 1992;6:2395–2408. - PubMed
    1. Buck M, Cannon W. Specific binding of the transcription factor sigma-54 to promoter DNA. Nature. 1992;358:422–424. - PubMed
    1. Buck M, Miller S, Drummond M, Dixon R. Upstream activator sequences are present in the promoters of nitrogen-fixation genes. Nature. 1986;320:374–378.

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