Biochemistry 1996, 35, 15715-15725
15715
A Direct Real-Time Spectroscopic Investigation of the Mechanism of Open Complex Formation by T7 RNA Polymerase† Srinivas S. Sastry* and Barbara M. Ross Laboratory of Molecular Genetics, Box 174, The Rockefeller UniVersity, New York, New York 10021 ReceiVed March 26, 1996; ReVised Manuscript ReceiVed October 10, 1996X
ABSTRACT: Initiation of transcription occurs through a series of steps starting with the binding of RNA polymerase to a promoter DNA and formation of a closed complex. The closed complexes, then isomerize to open complexes. In the open complexes a portion of the promoter DNA is unwound. Using fluorescence spectroscopy, we have investigated in real-time the mechanism of unwinding of promoter DNA during the transition from closed to open complexes of T7 RNA polymerase. We synthesized DNA templates containing the fluorescent base analog 2-aminopurine in place of adenine at specific positions in a T7 RNA polymerase promoter. We located the 2-aminopurine residues in the presumed melting domain of the promoter at -1, -4, and at -6. The fluorescence of 2-aminopurine increases when the DNA goes from a double-stranded form to a single-stranded form. By spectroscopically monitoring the increase in fluorescence of 2-aminopurine in DNA-T7 RNA polymerase complexes, we obtained kinetic and thermodynamic information for DNA unwinding. In the presence of the initiating nucleotide GTP, conformational transitions in the polymerase-promoter complex leading to strand opening were slower than in its absence. The rate of base pair disruption at -1, -6, and at -4 was also slower in the presence of GTP than in its absence. At 37 °C, base pair disruption occurred first at -1 followed by -6 and finally at -4. Open complex formation was temperature-sensitive. Temperature effects at -1, -6, and at -4 were consistent with this order of base pair disruption. The apparent activation energies (Ea) for base pair disruption around -1 and -6 were 14 kcal mol-1 and 50 kcal mol-1, respectively, also suggesting this order of base pair disruption. Transcription initiation assays using G-ladder synthesis revealed that initiation rates were almost the same on all three templates containing the modified base. Unlike strand opening, we did not observe lag times for G-ladder synthesis. We suggest that facile base pair disruption at -1 is sufficient for transcription initiation. Based on these data, it is proposed that the polymerase makes contacts at or near -1 and -6 resulting in untwisting of these base pairs thus creating at least two base pair disruption events at -1 and at -6, which are followed by bidirectional propagation to -4.
Initiation of procaryotic transcription involves a complex set of transitions beginning with the binding of RNA polymerase (R) to promoter DNA (P) (McClure, 1985). Equation 1 describes the overall mechanism of initiation of transcription. The recognition of the promoter leads to formation of closed complexes (RPc): k1
k2
-1
-2
NTPs
R + P {\ } RPc {\ } RPo 98 RNA k k
(1)
where k is a rate constant for the reaction step. In the closed complexes, the promoter DNA is in doublestranded form. The closed complexes, isomerize to open complexes, in which the DNA is partially melted (RPo) [for a review, see deHaseth and Helmann (1995)]. In the presence of NTPs, RPo begins synthesis of RNA. There are intermediates between RPc and RPo, and probably several types of complexes at each step depending on the promoter sequence, the temperature, and the ionic strength [for † S.S.S. is a Louis B. Mayer Foundation Fellow, and is grateful for a financial grant from the Mayer Foundation. We thank the HewlettPackard Co. for awarding an HPLC instrumentation grant and service contracts. * Corresponding author. Telephone: 212-327-8987. FAX: 212-3278651. E-Mail:
[email protected]. X Abstract published in AdVance ACS Abstracts, December 1, 1996.
S0006-2960(96)00729-5 CCC: $12.00
example, see Buc and McClure (1985), Cowing et al. (1989), Kovacic (1987), Krummel and Chamberlin (1989), Mecsas et al. (1991), Roe, et al. (1985), Sen and Dasgupta (1995), Spassky et al. (1985) and Suh et al. (1992a,b)]. While in the case of Escherichia coli RNAP it has been estimated that ∼17 base pairs (bp)1 of promoter DNA are disrupted in open complexes (Amouyal & Buc, 1987; deHaseth & Helmann, 1995; Gamper & Hearst, 1982), corresponding estimates for T7 RNAP have been less reliable. Although it has been implicitly accepted that the overall initiation reaction for T7 RNAP follows eq 1, so far RPc and RPo have not been experimentally separated nor have any intermediates been identified. Further complexities in the mechanism of T7 RNAP initiation were apparent from the fact that segments of the nontemplate strand in the promoter can be deleted without seemingly affecting the rates or the correctness of initiation (Maslak & Martin, 1993). We have investigated the mechanism of open complex formation using the fluorescence of 2-aminopurine as a probe. 2-AP is an analog of adenine that can form a Watson-Crick type of base pair with thymine in double1 Abbreviations: 2-AP, 2-aminopurine; T7 RNAP, bacteriophage T7 RNA polymerase; TBE, 180 mM Tris-borate-2 mM EDTA buffer; HPLC, high-performance liquid chromatography; ss, single-stranded; ds, double-stranded; bp, base pair(s); PC, personal computer; UM, unmodified template.
© 1996 American Chemical Society
15716 Biochemistry, Vol. 35, No. 49, 1996 stranded DNA (Figure 1A). The global structure of the DNA remains in B-form, and the substituted DNA is recognized by DNA-binding proteins (McLaughlin et al., 1987; Nordlund et al., 1989; Xu et al., 1994). In contrast to normal DNA bases, 2-AP exhibits strong fluorescence when excited at wavelengths above (>300 nm) the UV absorption range of normal DNA bases (
