RNA polymerase is an enzyme responsible for transcription. It copies genetic information from DNA into an RNA molecule, which then serves various functions within the cell, including carrying instructions for protein synthesis or acting directly in cellular processes. Precise guidance of RNA polymerase along the DNA strand is important for correct gene expression and cellular function.
Finding the Starting Line
RNA polymerase does not simply begin transcribing at any random point on the vast DNA molecule; it must first locate specific initiation sites. These starting points are marked by unique DNA sequences known as promoters, which act as signals for the enzyme to bind and begin its work.
In prokaryotic organisms, such as bacteria, a specialized protein called a sigma factor associates with the core RNA polymerase enzyme. This sigma factor directly recognizes and binds to specific sequences within the promoter, typically located around -10 base pairs (the Pribnow box, TATAAT) and -35 base pairs (TTGACA) upstream from the transcription start site.
Eukaryotic cells employ a more intricate mechanism to find the starting line, especially for RNA polymerase II, which transcribes protein-coding genes. This polymerase relies on a collection of general transcription factors, including TFIID, TFIIB, TFIIE, TFIIF, and TFIIH. These factors assemble at the promoter, often at a conserved TATA box sequence located approximately 25-30 base pairs upstream of the start site, with TFIID initiating the binding.
Selecting the DNA Template
Once RNA polymerase has accurately bound to the promoter, it faces the task of selecting the correct DNA strand to use as a template. A DNA double helix consists of two strands, but only one, known as the template strand or antisense strand, carries the genetic information to be transcribed into RNA. The other strand, the coding or sense strand, has a sequence similar to the resulting RNA.
The enzyme’s active site is precisely oriented to read the template strand in a specific direction, from its 3′ end towards its 5′ end. This directional reading dictates that the newly synthesized RNA molecule will be built in the opposite, 5′ to 3′ direction, adding nucleotides one by one. The promoter sequence itself contains inherent directional cues that guide this selection. The specific arrangement of DNA sequences within the promoter, along with the asymmetrical binding of associated proteins like sigma factors or general transcription factors, ensures that RNA polymerase is positioned to interact with only the correct template strand and to move in the proper direction.
Navigating Along the DNA Strand
After successfully initiating transcription, RNA polymerase transitions into the elongation phase, moving steadily along the DNA strand. During this stage, the enzyme locally unwinds a short segment of the DNA double helix, typically about 10-17 base pairs, forming a temporary structure known as the transcription bubble. Within this bubble, the template DNA strand becomes accessible for base pairing with incoming ribonucleotides.
As the polymerase moves, it continuously adds complementary RNA nucleotides to the growing RNA chain, strictly following the base-pairing rules (adenine with uracil, guanine with cytosine). The enzyme maintains a strong and stable association with the DNA template throughout this process, a characteristic known as processivity. This ensures that transcription proceeds over long stretches of DNA without the enzyme detaching.
The RNA polymerase itself functions as a molecular motor, driven by the energy released from nucleotide triphosphate hydrolysis. It moves forward, unwinding DNA ahead of it and allowing the DNA strands to re-anneal behind it, effectively closing the transcription bubble. This continuous unwinding and re-annealing of the DNA helix provides the physical track that guides the polymerase, ensuring it stays precisely on course and accurately synthesizes the RNA transcript.
Variations Across Life Forms
While the fundamental mechanism of RNA polymerase guidance is conserved, significant differences exist between prokaryotic and eukaryotic cells, reflecting their genomic complexities. Prokaryotes, like bacteria, typically possess a single type of RNA polymerase responsible for transcribing all classes of RNA. Its guidance relies primarily on the direct interaction of sigma factors with specific promoter sequences, a relatively straightforward and efficient system.
Eukaryotic cells, in contrast, utilize multiple distinct RNA polymerases, each dedicated to transcribing different types of RNA. RNA polymerase I transcribes ribosomal RNA genes, RNA polymerase III transcribes transfer RNA and some small nuclear RNA genes, while RNA polymerase II is responsible for transcribing all protein-coding genes. This division of labor allows for more precise regulation of gene expression.
The guidance of eukaryotic RNA polymerase II is particularly elaborate, involving a large array of general transcription factors. Beyond these, eukaryotic transcription initiation is further influenced by distant regulatory DNA sequences called enhancers and silencers. Specific activator or repressor proteins bind to these elements, interacting with the promoter-bound complex to fine-tune polymerase recruitment and activity. Moreover, the organization of eukaryotic DNA into chromatin, involving DNA wrapped around histone proteins, adds an additional layer of guidance. Chromatin structure can either block or facilitate access for RNA polymerase and its associated factors, influencing where transcription can occur.