Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
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

PubMed Disclaimer

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.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

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.

Publication types

MeSH terms

LinkOut - more resources