Published in: Science, vol. 289, no. 5479, pp. 619-624 (July 28, 2000):

A Structural Model of Transcription Elongation".

Nataliya Korzheva 1, Arkady Mustaev 1, Maxim Kozlov 1, Arun Malhotra 2, Vadim Nikiforov 3, Alex Goldfarb 1, and Seth A. Darst 4*.

1 Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA,
2 Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33101, USA.
3 Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia,
4 Rockefeller University, 1230 York Avenue, New York, NY 10012, USA.

* To whom correspondence should be addressed. E-mail: darst@rockvax.rockefeller.edu


Abstract:
Fig. 2:
Cited References and Notes:
Additional References:
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Abstract:

The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the b' subunit and enclosed on top by the b subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the b subunit harboring rifampicin resistance mutations, to the b' subunit "rudder". The single-stranded RNA is then extruded through another channel formed by the b-subunit flap domain. The model provides insight into the functional properties of the transcription complex.



Fig. 2: Nucleic acid scaffold of the transcription complex and its contacts with RNAP subunits. Horizontal bars represent E. coli b (top) and b' (bottom) subunits. Lettered gray boxes indicate evolutionarily conserved regions (1). Dispensible regions [DR (34)] and split sites [SS (37)] are indicated. Nucleic acid scaffold of the transcription complex is shown in the middle. Filled circles represent the DNA (red, template strand; yellow, nontemplate strand) and RNA (gold) chains. The incoming nucleotide substrate is green. Open circles show the segment of single-starnd downstream RNA in the backtracked TEC. The positions of nucleotide residues are numbered relative to the i + 1 site of the active center, which is denoted +1. The 12- to 14-base transcription bubble is indicated (10, 11). Results of chemical and enzymatic footprinting of the DNA and RNA are also indicated by gray shading (11-13). Lines connect contacts and protein segments (indicated by cross-hatching) of RNAP subunits (7, 30). Lysine residues that are targets of Lys-specific cross-linking are numbered. Colored triangles show segments of nucleic acid scaffold that cross-link to the same protein regions.

Cited References and Notes:

1. Sweetser D, Nonet M, Young RA, Proc. Natl. Acad. Sci. U.S.A., 84: 1192 (1987);
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7. See supplementary material at Science Online at
http://www.sciencemag.org/feature/data/1051897.shl

10. Siebenlist U, Simpson RB, Gilbert W, Cell 20: 269 (1980);
Kirkgaard K, Buc H, Spassky A, Wang JC, Proc. Natl. Acad. Sci. U.S.A., 80: 2544 (1983);
Mecsas J, Cowing DW, Gross CA, J. Mol. Biol. 220: 585 (1991).

11. Zaychikov E, Denissova L, Heumann H, Proc. Natl. Acad. Sci. U.S.A., 92: 1739 (1995).

12. Wang D, and Landick R, J. Biol. Chem. 272: 5989 (1997).

13. Monforte JA, Kahn JD, Hearst JE, Biochemistry 29: 7882 (1990);
Komissarova N, and Kashlev M, J. Proc. Natl. Acad. Sci. U.S.A., 95: 15329 (1998).

30. Borukhov S, Lee J, Goldfarb A, J. Biol. Chem. 266: 23932 (1991);
Markovstov V, Mustaev A, Goldfarb A, Proc. Natl. Acad. Sci. U.S.A., 93: 3221 (1996);
Epshtein V, et al, in preparation.

34. Borukhov S, et al, J. Biol. Chem. 266: 23921 (1991);
Severinov K, et al, J. Biol. Chem. 269: 14254 (1994).

37. Severinov K, et al, Proc. Natl. Acad. Sci. U.S.A., 92: 4591 (1995);
Severinov K, et al, J. Biol. Chem. 271: 27969 (1996).


Additional References:

"A Model of Specific De-Repression within Interphase Chromatin".

"Mated Models of Gene Regukation in Eukaryotes".

"Oncogenes as Molecular Targets within Active Chromatin".


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