[1] Promoters and basal transcription machinery in eubacteria and eukaryotes: Concepts, definitions, and analogies

Jan S Fassler; Gary N Gussin

doi:10.1016/S0076-6879(96)73003-3

In eubacteria, the interaction of each of several (5–10) σ factors with a single core polymerase determines the promoter specificity of the corresponding holoenzyme; in contrast, in eukaryotes the most obvious specificity determinant is the existence of three “core” polymerases, which differ in the specificity with which they interact with particular TBP-containing complexes. For Pol II, the interaction is mediated by TFIIB, which contacts both RNAP and specific TAFs; for Pol III, the same function may be served by BRF (B-related factor), a component of TFIIIB. Presumably, a similar factor is necessary for interaction of TBP-containing complexes with Pol I. In both eubacteria and prokaryotes, promoter specificity is further determined by the presence of regulators of initiation—activators or repressors—capable, usually, of responding to particular metabolic, developmental, or environmental cues. We define a eubacterial promoter as the minimal set of sequence elements necessary for specific recognition and initiation by RNA polymerase holoenzyme. The problem in applying a similar definition to eukaryotic promoters is the difficulty in identifying a eukaryotic holoenzyme that is functionally analogous to Eσ70. However, the plethora of factors required for full expression of eukaryotic transcription units compels us to find a common way of conceptualizing the roles of each set of factors in promoter site selection (Fig. 1). We start from the following premises: (1) because the common task at all eukaryotic promoters seems to be getting TBP to the DNA—in either a specific, TATA-binding or a nonspecific TATA-less-binding form—the eukaryotic counterpart to the eubacterial holoenzyme ought to include what is minimally needed for TBP binding (specifically or nonspecifically) to DNA and its association with RNAP; (2) promoters that contain no apparent TATA sequence are functionally analogous to weak eubacterial promoters that require activators for maximal expression. According to this view, Pol I, II, and III are analogous to eubacterial core polymerase, while TBP and the protein(s) that mediate its association with the core are analogous to σ. Although elongation factors may bind to the eukaryotic polymerases, they are equivalent to proteins such as the termination factor ϱ and Nus proteins, which bind at various times to Eσ70, but are not part of the holoenzyme. Thus, if fully assembled, functional counterparts to E. coli holoenzymes exist in eukaryotes, they should consist of (1) Pol I “core” enzyme, TBP, one or more additional components of the SL1 complex, and possibly a TFIIB-like factor, (2) Pol II “core” enzyme, TBP and one or more TAFs, TFIIB, Inr-recognition protein(s), and possibly TFIIA and TFIIF, and (3) Pol III “core” enzyme, TBP, BRF, and one or more additional components of TFIIIB. The fit to the eubacterial holoenzyme model is least comfortable in the case of Pol III. It seems reasonable to exclude TFIIIA, which is necessary only for class 1 promoters, and is dispensible once TFIIIB is bound to the DNA; similar reasoning leads us to exclude TFIIIC, which is not necessary for TATA-containing class 3 promoters. In some cases, the distinction between proteins that function essentially as activators and those that are essential components of an initiation-competent holoenzyme may turn out to be semantic, but it seems useful to bear the distinction in mind to help anticipate what kinds of preassembled, fully functional complexes might be found in eukaryotic cells. Conceptual analogies between eubacterial and eukaryotic enzymes may also be helpful in understanding eventually how the enzymes evolved, including the evolution of pathways for assembling different functional units. For example, the carboxy-terminal domain of the E. coli RNAP α subunit is functionally equivalent to eukaryotic coactivators, the main differences being that it is covalently attached to the holoenzyme and has evolved a sequence-specific DNA-recognition capability. Strong functional and amino acid sequence similarities between eubacterial and eukaryotic polymerases should not be surprising because the characteristic activities of the enzymes are the same. The basal transcription machinery should have evolved relatively early, but should be constrained in evolution by selection against even small changes in recognition specificity, in order to preserve fidelity in the quantity and quality of RNA molecules synthesized. Discoveries of strong similarities between transcription factors and polymerases of Archaea and those of eukaryotes provide an argument in favor of the idea that once the basic transcription apparatus emerged, the ways in which it could evolve were limited.

[1] Promoters and basal transcription machinery in eubacteria and eukaryotes: Concepts, definitions, and analogies

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