Prokaryotic Gene Transcription : Prokaryotic RNA polymerase

The structure of magnesium-requiring RNA polymerase (RNA pol), the signals that control transcription, and the varieties of modification that RNA transcripts can undergo differ among organisms, particularly from prokaryotes to eukaryotes. Therefore, the discussions of prokaryotic and eukaryotic transcription are presented separately.
 Prokaryotic RNA polymerase
In bacteria, one species of RNA pol synthesizes all of the RNA except for the short RNA primers needed for DNA replication [Note: RNA primers are synthesized by the specialized, monomeric enzyme primase .] RNA pol is a multisubunit enzyme that recognizes a nucleotide sequence (the promoter region) at the beginning of a length of DNA that is to be transcribed. It next makes a complementary RNA copy of the DNA
template strand and then recognizes the end of the DNA sequence to be transcribed (the termination region). RNA is synthesized from its 5′-end to its 3′-end, antiparallel to its DNA template strand . The template is copied as it is in DNA synthesis, in which a guanine (G) on the DNA specifies a cytosine (C) in the RNA, a C specifies a G, a thymine (T) specifies an adenine (A), but an A specifies a uracil (U) instead of a T (Fig.1). The RNA, then, is complementary to the DNA template (antisense, minus) strand and identical to the coding (sense, plus) strand, with U replacing T. Within the DNA molecule, regions of both strands can serve as templates for transcription. For a given gene, however, only one of the two DNA strands can be the template. Which strand is used is determined by the location of the promoter for that gene. Transcription by RNA pol involves a core enzyme and several auxiliary proteins.

Figure 1: Antiparallel, complementary base pairs between DNA and RNA. T = thymine; A = adenine; C = cytosine; G = guanine; U = uracil.
1. Core enzyme: Five of the enzyme’s peptide subunits, 2 α, 1 β, 1 β′, and 1 Ω, are required for enzyme assembly (α, Ω), template binding (β′), and the 5′→3′ polymerase activity (β) and together are referred to as the core enzyme (Fig. 2). However, this enzyme lacks specificity (that is, it cannot recognize the promoter region on the DNA template).

Figure 2: Components of prokaryotic RNA polymerase.
2. Holoenzyme: The σ subunit (sigma factor) enables RNA pol to recognize promoter regions on the DNA. The σ subunit plus the core enzyme make up the holoenzyme. [Note: Different σ factors recognize different groups of genes, with σ70 predominating.]