- DNA-dependent RNA polymerase (DdRp) is a fundamental enzyme in all living organisms that synthesizes RNA using a DNA template. This process, known as transcription, is the first step in gene expression and is essential for the production of messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and other non-coding RNAs. DdRp reads the DNA sequence and assembles a complementary RNA strand, playing a central role in translating genetic information from the genome into functional molecules.
- In prokaryotes, such as bacteria, transcription is carried out by a single type of DNA-dependent RNA polymerase. This enzyme consists of a core enzyme made up of five subunits (α₂ββ′ω) and a sigma (σ) factor that is required for promoter recognition and transcription initiation. Once transcription begins, the sigma factor is often released, and the core enzyme continues elongation. The bacterial RNA polymerase binds to specific promoter regions on the DNA, unwinds the DNA helix, and catalyzes the addition of ribonucleotides complementary to the DNA template strand. The enzyme proceeds until it encounters a termination signal, at which point the RNA transcript is released.
- In eukaryotes, transcription is more complex and involves three main types of nuclear DNA-dependent RNA polymerases:
- RNA polymerase I (Pol I): transcribes most ribosomal RNA (rRNA) genes.
- RNA polymerase II (Pol II): transcribes protein-coding genes into mRNA and also produces some small nuclear RNAs (snRNAs).
- RNA polymerase III (Pol III): transcribes tRNAs, 5S rRNA, and other small RNAs.
- Each eukaryotic polymerase is a large multi-subunit complex and requires a distinct set of general transcription factors to initiate transcription at specific promoters. For instance, Pol II requires factors such as TFIID, TFIIB, TFIIF, TFIIE, and TFIIH, which help in promoter recognition, DNA melting, and polymerase recruitment. Unlike prokaryotes, eukaryotic transcription is closely coupled with RNA processing, including capping, splicing, and polyadenylation, all of which are coordinated by Pol II’s C-terminal domain (CTD).
- Structurally, DNA-dependent RNA polymerases share a conserved catalytic core that resembles a crab claw, with a cleft where the DNA template is read and the RNA strand is synthesized. The active site contains conserved motifs, including magnesium-binding aspartate residues, which catalyze the formation of phosphodiester bonds. The enzyme moves along the DNA template in the 3′ to 5′ direction, synthesizing RNA in the 5′ to 3′ direction.
- Viruses, particularly DNA viruses such as poxviruses and adenoviruses, may encode their own DNA-dependent RNA polymerases if they replicate outside the host nucleus (e.g., in the cytoplasm), where they cannot access the host’s nuclear transcription machinery. These viral polymerases resemble simplified versions of their cellular counterparts and are adapted for rapid transcription of viral genes under compact regulatory control.
- DNA-dependent RNA polymerases are essential not only for normal cellular function but also for regulatory processes such as development, environmental responses, and cell differentiation. Their activity is tightly regulated through multiple mechanisms, including promoter accessibility, chromatin modifications, transcription factor binding, and feedback from the products of transcription.
- From a biotechnological perspective, DdRps have been instrumental in in vitro transcription systems. Bacteriophage-derived RNA polymerases such as T7, SP6, and T3 RNA polymerases—which are highly specific, single-subunit DNA-dependent RNA polymerases—are widely used in molecular biology to produce RNA transcripts for research, vaccines, and therapeutic applications.
