Recall that DNA replication requires a number of different enzymes and proteins. Transcription might initially appear to be quite different because a single enzyme—RNA polymerase—carries out all the required steps of transcription, but on closer inspection, the processes are actually similar. The action of RNA polymerase is enhanced by a number of accessory proteins that join and leave the polymerase at different stages of the process. Each accessory protein is responsible for providing or regulating a special function. Thus, transcription, like replication, requires an array of proteins.

BACTERIAL RNA POLYMERASE Bacterial cells typically possess only one type of RNA polymerase, which catalyzes the synthesis of all classes of bacterial RNA: mRNA, tRNA, and rRNA. Bacterial RNA polymerase is a large, multimeric enzyme (meaning that it consists of several polypeptide chains).

At the heart of most bacterial RNA polymerases are five subunits (individual polypeptide chains) that make up the core enzyme. This enzyme catalyzes the elongation of the RNA molecule by the addition of RNA nucleotides. Other functional subunits join and leave the core enzyme at particular stages of the transcription process. The sigma (σ) factor controls the binding of RNA polymerase to the promoter. Without sigma, RNA polymerase will initiate transcription at a random point along the DNA. After sigma has associated with the core enzyme (forming a holoenzyme), RNA polymerase binds stably only to the promoter region and initiates transcription at the proper start site. Sigma is required only for promoter binding and initiation; after a few RNA nucleotides have been joined together, sigma usually detaches from the core enzyme. Many bacteria have multiple types of sigma factors; each type of sigma initiates the binding of RNA polymerase to a particular set of promoters.

Rifamycins are a group of antibiotics that kill bacterial cells by inhibiting RNA polymerase. These antibiotics are widely used to treat tuberculosis, a disease that kills almost 2 million people worldwide each year. The structures of bacterial and eukaryotic RNA polymerases are sufficiently different that rifamycins inhibit bacterial RNA polymerases without interfering with eukaryotic RNA polymerases. Recent research has demonstrated that several rifamycins work by binding to and jamming the part of the bacterial RNA polymerase that clamps onto DNA, thus preventing the RNA polymerase from interacting with the promoter on the DNA.

EUKARYOTIC RNA POLYMERASES Most eukaryotic cells possess three distinct types of RNA polymerase, each of which is responsible for transcribing a different class of RNA: RNA polymerase I transcribes rRNA; RNA polymerase II transcribes pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs; and RNA polymerase III transcribes other small RNA molecules—specifically, tRNAs, small rRNAs, some miRNAs, and some snRNAs (Table 10.3). RNA polymerases I, II, and III are found in all eukaryotes. Two additional RNA polymerases, named RNA polymerase IV and RNA polymerase V, have been found in plants. These RNA polymerases transcribe RNAs that play a role in DNA methylation and chromatin structure.

All eukaryotic polymerases are large, multimeric enzymes, typically consisting of more than a dozen subunits. Some subunits are common to all RNA polymerases, whereas others are limited to one type of polymerase. As in bacterial cells, a number of accessory proteins bind to the core enzyme and affect its function.

CONCEPTS