Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase

Abstract

At Class II catabolite activator protein (CAP)-dependent promoters, CAP activates transcription from a DNA site overlapping the DNA site for RNA polymerase. We show that transcription activation at Class II CAP-dependent promoters requires not only the previously characterized interaction between an activating region of CAP and the RNA polymerase alpha subunit C-terminal domain, but also an interaction between a second, promoter-class-specific activating region of CAP and the RNA polymerase alpha subunit N-terminal domain. We further show that the two interactions affect different steps in transcription initiation. Transcription activation at Class II CAP-dependent promoters provides a paradigm for understanding how an activator can make multiple interactions with the transcription machinery, each interaction being responsible for a specific mechanistic consequence.

Figure 1. CAP Has a Class-II-Specific Activating Region (“AR2”)

(A) Transcription activation at the Class II CAP-dependent promoter CC(−41.5) (in vitro). (B) Transcription activation at the Class I CAP-dependent promoter CC(−61.5) (in vitro). (C) DNA binding (means ± 2 SD). (D) DNA bending (means ± 2 SEM). (E) Structure of the CAP–DNA complex showing activating regions. The figure illustrates the crystallographic structure of the CAP–DNA complex at 2.5 Å resolution (Schultz et al., 1991; Parkinson et al., 1996). CAP is in light blue. DNA and cAMP are in red. AR1 is in blue (amino acids 156–164). AR2 is in green (amino acids 19, 21, and 101 in dark green; amino acid 96 in light green). Amino acid 52, a site at which substitutions result in improved transcription activation at Class II CAP-dependent promoters (Bell et al., 1990; Williams et al., 1991), is in yellow.

Figure 2. AR2 Requires Positive Charge

(A) Effects of alanine substitution on transcription activation at the Class II CAP-dependent promoter CC(−41.5) (activation_CAP/activation_X). Substitution of His-19, His-21, or Lys-101 results in a >5-fold defect in transcription activation; substitution of Glu-96 results in a ≥3-fold improvement in transcription activation (asterisk). (B) Effects of alanine substitution on transcription activation at the Class I CAP-dependent promoter CC(−61.5) (activation_CAP/activation_X). (C) Effects of alanine substitution on transcription repression at an artificial CAP-repressed promoter (repression_CAP/repression_X ).

Figure 3. AR2 Functions in the Downstream Subunit of CAP

(A) Expected orientations of CAP heterodimers at the CX(−41.5) and XC(−41.5) promoters (see Zhou et al., 1993b, 1994b). L19, Y19, and E101 denote [Leu-19]CAP, [Tyr-19] CAP, and [Glu-101]CAP subunits (nonfunctional AR2, wild-type DNA-binding specificity). V181 denotes the [Val-181]CAP subunit (functional AR2, non-wild-type DNA-binding specificity). Promoter −35 and −10 elements are shown as bars; transcription start points are shown as arrows. (B) Transcription activation by oriented heterodimers (determined in vivo as in Zhou et al., 1994b).

Figure 4. AR2 Functions through Protein–Protein Interaction with RNAP

Fluorescence anisotropy analysis of interaction of RNAP with a pre-formed binary complex of CAP and a fluorescein-labeled DNA fragment containing the consensus DNA site for CAP (DNA fragment ICAP42FL of Heyduk et al., 1993). Data are shown for wild-type CAP (filled circles), [Ala-158]CAP (AR1⁻; open circles), [Leu-19]CAP (AR2⁻; open triangles), [Tyr-19]CAP (AR2⁻; open inverted triangles), [Glu-101]CAP (AR2⁻; open diamonds), and [Asn-52]CAP (a mutant superfunctional in transcription activation at Class II CAP-dependent promoters [Bell et al., 1990; Williams et al., 1991]; open squares). Data are expressed as (A − A₀)/A₀, where A denotes fluorescence anisotropy in the presence of RNAP and CAP, and A₀ denotes fluorescence anisotropy in the absence of RNAP and CAP.

Figure 5. AR2 Interactswith the RNAP α Subunit N-Terminal Domain

(A) Site-specific protein–protein photocross-linking followed by cleavage and radiolabel transfer. Lane 1, photocross-linking reaction; lane 2, control reaction omitting RNAP; lane 3, control reaction omitting UV-irradiation. Radiolabeled CAP is the product of intramolecular cross-linking; radiolabeled α is the result of intermolecular CAP→α photocross-linking. (B) Proteolytic mapping. Lane 1, radiolabeled α (see A); lane 2, hydroxylamine digest of radiolabeled α.

Figure 6. AR2 Interacts with Amino Acids 162–165 of RNAP α Subunit N-Terminal Domain

(A) Substitutions within RNAP α subunit that result in specific defects in Class II CAP-dependent transcription (Glu-165→Lys, Glu-162→Ala, Glu-163→Ala, Asp-164→Ala, Glu-165→Ala; −, large defect in vivo; ±, small, but reproducible, defect in vivo). αNTD, αCTD, and linker denote the α N-terminal domain, the α C-terminal domain, and the interdomain linker, respectively (Blatter et al., 1994; Busby and Ebright, 1994). (B) Class II CAP-dependent transcription at CC(−41.5) (in vitro). (C) Class I CAP-dependent transcription at CC(−61.5) (in vitro). (D) CAP-independent transcription at lacUV5 (in vitro).

Figure 7. AR1 and AR2 Affect Different Steps in Transcription Initiation

(A) τ-plot comparing Class II CAP-dependent transcription with wild-type CAP (filled circles), [Ala-158]CAP (AR1⁻; open circles), and [Glu-101]CAP (AR2⁻; open triangles). Data plotted are means of three independent determinations (± 1 SD). Slopes = (K_Bk_f)⁻¹; y-intercepts = (k_f)⁻¹ (McClure, 1980). (B) Values of K_B and k_f.

Figure 8. Mechanism of Transcription Activation at Class II CAP-Dependent Promoters

There are two mechanistic components to transcription activation at Class II CAP-dependent promoters: anti-inhibition (mediated by interaction of AR1 with αCTD) and direct activation (mediated by interaction of AR2 with αNTD). (A) Model of the ternary complex of CAP, RNAP, and a Class II CAP-dependent promoter. AR1 (functional in upstream subunit of CAP) is indicated by a filled circle. AR2 (functional in downstream subunit of CAP) is not visible in this orientation but would be located directly beneath the “N” of “αNTD.” (B) As (A), but omitting RNAP α subunit.