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Note: The subuniis in each colum»'. are ((Sled in order of decreasing molecular weight Source Data adapted from Ebright R.H 2000 J. MoI. Bid 304: 687 696, Fro. t. p 606. © 2000 Academic Press

Note: The subuniis in each colum»'. are ((Sled in order of decreasing molecular weight Source Data adapted from Ebright R.H 2000 J. MoI. Bid 304: 687 696, Fro. t. p 606. © 2000 Academic Press essentially all protein-encoding genes. Pol I and Pol HI are each involved in transcribing specialized, RNA-encoding genes, Specifically. Pol I transcribes the large ri bosom a! RNA precursor gene, whereas Pol I1T transcribes tRNA genes, some small nuclear RNA genes, and the 5S rRNA gene. We return to these enzymes at the end of the chapter.

The bacterial RNA polymerase core enzyme alone is capable of synthesizing RNA and comprises two copies cf the u subunit and one each of the p, p', and w subunits. That enzyme is closely related to the eukaryotic polymerases (see Table 12-1). Specifically, the two large subunits, p and ¡3', are homologous to the two large subunits found in RNA Pol II (RPB1 and RPB2). The a subunits are homologous to RPB3 and RPBll and w to RPB6. The structure of a bacterial RNA polymerase core enzyme is similar to that of the yeast Pol II enzyme. These are shown side-by-side in Figure 12-2. Later we wilJ describe some of the structural details that shed light on how these enzymes work. For now we just highlight some of the general features.

The bacterial and yeast enzymes share an overall shape and organization; indeed, they are more alike than the comparison of the subunit sequences would predict. This is particularly true of the internal parts, near the active site, and less so on the peripheries. The distribution cif these similarities and differences presumably reflects, in. the former case, the fact that the enzymes carry out the same Function (synthesis of RNA on a DNA template), and in the latter case, that, to function in the cell, the two enzymes interact with other proteins and those are specific and different in the two cases, as we shall see.

Overall, the shape of each enzyme resembles a crab claw. This is reminiscent of the "hand" structure of DNA polymerases described in Chapter B (Figure 8-5). The fwo pincers of the crab claw are made up predominantly of the two largest subunits of each enzyme (p' and [3 for the bacterial case, RPBl and RPB2 for the eukaryotic enzyme). The active site, which is made up of regions from both these subunits, is found at the base of the pincers within a region called the "active center cleft" (see Figure 12-2). The active site can bind two Mg^' ions, consistent with the proposed two-metal ion catalytic mechanism for nucleotide addition proposed for all types of polymerase (see Chapter 8).

FIGURE 12-2 Comparison of the crystal structures of prokaryotic and eukaryotic RNA polymerases, (a) Structure of RNA polymerase core enzyme from T aquaticus. The sub-units are coioted as fdlows: fi is shown iri pur pie, p' in blue, the two a subunits in ydlow and green, and oj in red (Seth Darst, The Rockefeller University, personal communication.) (b) Structure of RNA Polymerase II from yeast 5. cere-visiae. The subunits are colored to show their relatedness to those in the bactenal enzyme (see Table 12-1). Thus, RPB 1 and 2 are shown in purple and blue respectively; RPB3 and H are shown m yellow and green; and RPB6 in red (Cramer P., Bushnell D.A, arid Kornberg RD. 2001 Science 292: 1863) Images prepared with MolScript, BobScnpt, and Raster 3D,

There are various channels (hat allow DNA, RNA, and ribonucleotides into and out of the enzyme's active center cleft. These we discuss later when considering the mechanisms of transcription.

Transcription by RNA Polymerase Proceeds in a Series of Steps

To transcribe a gene. RNA polymerase proceeds through a series of well-defined steps which are grouped into three phases: initiation, elongation, and termination. Here, and in Figure 12-3, we summarize the basic features of each phase.

Initiation. A promoter is the DNA sequence that initially binds the RNA polymerase (together with initiation factors in many cases). Once formed, the promoter-polymerase complex undergoes structural changes required for initiation to proceed. As in replication initiation, the DNA around the point where transcription will start unwinds, and the base

RNA Polymerases and the Transcription Cycle 351

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