RNA polymerase is an enzyme that synthesizes RNA from a DNA template. This process, known as transcription, is the first step in gene expression, converting the information stored in DNA into a functional product like a protein. The enzyme reads the genetic code within DNA and produces a complementary RNA strand, enabling cells to produce the molecules necessary for their functions.
This molecular machine performs several complex tasks. RNA polymerase recognizes specific start and stop sequences on the DNA to ensure it transcribes the correct segments. It also has proofreading capabilities to maintain the accuracy of the RNA sequence. By responding to cellular signals, the enzyme controls which genes are expressed and when, a process that directs cellular function and development.
How RNA Polymerase Builds RNA
The construction of an RNA molecule by RNA polymerase is a precise process using a single strand of the DNA double helix as a guide. Before transcription can begin, the enzyme must locate the correct starting point on the DNA. This is achieved by recognizing and binding to a specific DNA sequence known as a promoter, which acts as a signal for the start of a gene.
Once bound to the promoter, the process of initiation begins. The RNA polymerase unwinds a small section of the DNA double helix, exposing the nucleotide bases on each strand. This creates a “transcription bubble” and allows one of the DNA strands to serve as the template for the new RNA molecule. This initial step is highly controlled to ensure the enzyme is correctly positioned before synthesis starts.
Following initiation, the enzyme moves into the elongation phase, where it travels along the DNA template strand. As it moves, RNA polymerase reads the DNA sequence one base at a time and adds a corresponding RNA nucleotide to the growing RNA chain. The new RNA strand is built in the 5′ to 3′ direction, and for each adenine (A) on the DNA template, a uracil (U) is added to the RNA strand instead of thymine (T). This process allows the enzyme to synthesize long RNA chains without detaching from the DNA.
The final stage of this process is termination. RNA polymerase continues to move along the DNA until it encounters a specific sequence known as a terminator, which signals that the RNA transcript is complete. Upon reaching the terminator, the enzyme stops adding nucleotides, releases the newly synthesized RNA molecule, and detaches from the DNA template. The DNA double helix then reforms.
The Diverse Family of RNA Polymerases
The machinery for transcription is not uniform across all life, with a distinction between prokaryotic and eukaryotic organisms. In prokaryotes, such as bacteria, a single type of RNA polymerase is responsible for synthesizing all classes of RNA, including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
Eukaryotic cells, on the other hand, exhibit greater specialization, employing multiple distinct RNA polymerases with specific functions. This division of labor allows for more intricate control over gene expression. Eukaryotes have three main types of RNA polymerase in their nucleus, each responsible for transcribing different sets of genes.
The main enzymes are designated RNA Polymerase I, II, and III. RNA Polymerase I is located in the nucleolus and is dedicated to synthesizing most of the ribosomal RNA (rRNA), which are components of ribosomes. RNA Polymerase II is responsible for synthesizing all protein-coding messenger RNA (mRNA), as well as most small nuclear RNAs (snRNAs) and microRNAs (miRNAs), which are involved in gene regulation.
RNA Polymerase III synthesizes transfer RNA (tRNA), which is responsible for carrying amino acids to the ribosome during protein synthesis. It also produces the 5S rRNA component of the ribosome and other small RNAs. This specialization means that each polymerase recognizes different types of promoters and works with distinct sets of accessory proteins.
Regulating RNA Polymerase Activity
The activity of RNA polymerase is not constant; it is regulated to ensure that genes are expressed at the right time and in the appropriate amounts. This control is important for processes ranging from embryonic development to a cell’s response to environmental changes. The cell employs proteins and DNA sequences to direct the enzyme’s work, ensuring that specific sets of genes are turned on or off as needed.
A primary method of regulation involves proteins called transcription factors. These proteins bind to specific DNA sequences and can either help recruit RNA polymerase to a gene’s promoter, acting as activators, or block its access, acting as repressors. This interplay between activators and repressors allows the cell to fine-tune the level of transcription for thousands of genes.
Besides the core promoter where RNA polymerase binds, other sequences called enhancers and silencers can be located far away from the gene they influence. Enhancers can be bound by activator proteins, and through the looping of DNA, these enhancers can be brought into close physical proximity with the promoter to stimulate transcription. Silencers work in a similar but opposite fashion, binding repressor proteins to inhibit transcription.
The physical state of the DNA itself provides another layer of regulation. In eukaryotic cells, DNA is packaged with proteins into a structure called chromatin. The tightness of this packaging can determine whether a gene is accessible to RNA polymerase and transcription factors. “Open” chromatin is loosely packed and allows for active transcription, whereas “closed” chromatin makes the DNA inaccessible, silencing the genes within that region.
RNA Polymerase in Sickness and Health
The precise function of RNA polymerase is directly linked to an organism’s health, and disruptions in its activity can lead to disease. For example, uncontrolled transcription of genes that promote cell growth can contribute to the development of cancer. Some genetic developmental disorders are also traced back to mutations affecting the function of RNA polymerase or its associated regulatory factors.
Because of its role in bacterial life, RNA polymerase is a target for antibiotics. The structure of bacterial RNA polymerase is different enough from its eukaryotic counterparts that drugs can be designed to inhibit the bacterial enzyme specifically, without harming human cells. The antibiotic rifampicin, for instance, binds to the bacterial RNA polymerase and physically blocks the path of the growing RNA chain, thereby halting transcription and killing the bacteria.
Viruses, which rely on the host cell’s machinery to replicate, also interact with RNA polymerase. Some viruses use the host cell’s RNA polymerase to transcribe their own genes, while others bring their own polymerase enzymes with them. These viral polymerases can also be targets for antiviral drugs, offering a way to stop viral replication.
Nature also provides examples of toxins that target this enzyme. One of the most well-known is alpha-amanitin, a toxin produced by the death cap mushroom (Amanita phalloides). This substance is an inhibitor of eukaryotic RNA Polymerase II, the enzyme responsible for producing messenger RNA. Ingestion of this toxin leads to a shutdown of protein production in cells, causing massive liver and kidney failure, which is often fatal.