RNA Polymerase Definition
RNA polymerase is the protein which synthesizes new RNA strands by transcribing the DNA sequence into RNA. This RNA molecule is then processed and read by a ribosome to produce a protein. RNA polymerase is found in all living organisms because of its importance to the processes of life. Slight differences are found between different types of RNA polymerase, and eukaryotes even have several different versions which process different parts of the DNA.
RNA Polymerase Function
RNA polymerase is the most important enzyme in the process of transcription. Remember that transcription is the process of copying the double-stranded DNA into a single strand of RNA. They may look slightly different, but they are both written in the language of nucleotides. In order for RNA polymerase to begin its work, it must first find an appropriate promoter region. This region can be targeted by transcription factors in eukaryotes. These proteins bind to the site, creating a suitable arrangement for RNA polymerase to bind and start transcription. In bacteria, there is only a single promoter, the sigma initiation factor. This process can be seen with the generalized RNA polymerize molecule shown below transcribing DNA. The transcription factors are not shown.
As RNA polymerase binds to the DNA, it changes conformation, or shape. This starts the enzymatic chain reaction which grows a new chain of nucleotides into an RNA molecule based off of the template presented. After RNA polymerase has created this new molecule, the RNA must be processed and released from the nucleus. Now called messenger RNA, or mRNA, it will encounter a ribosome which has the appropriate mechanisms for the process of translation.
Much like translating English to Spanish, the ribosome must “read” the sequence of the RNA and convert the message into the language of amino acids. These small molecules form long chains, which fold into intricate shapes to become biochemically active proteins. These proteins, in turn, create and maintain parts of the DNA, as well as replicate the DNA. Parts of the DNA store the genetic information for the RNA polymerase protein itself, which is first decoded by an RNA polymerase molecule. This situation is really the basis of the chicken and the egg if you think about it.
RNA Polymerase Structure
In Humans and Eukaryotes
Humans share a similar RNA polymerase structure with the rest of the eukaryotes with membrane-bound organelles. Though there are several different types, the overall structure is similar in each.
Like many eukaryotes, humans carry 3 different versions of RNA polymerase, identified by Roman numerals. RNA polymerase I specifically encodes the majority of the RNA used within ribosomes for them to attach to and decode RNA sequences. RNA polymerase II synthesizes most mRNAs and is responsible for transcribing the majority of the genetic code. It is also the largest, containing 12 subunits. RNA polymerase III synthesizes transfer RNA, which are small segments attached to free-floating amino acids to help the ribosome recognize them when they are bound into a protein.
Plants have two other RNA polymerase enzymes, with functions related to producing RNA which suppresses other genes. This is a form of gene regulation not seen in other eukaryotes, and which depends on a special form of RNA polymerase, but it gives plants the ability for more gene regulation.
In Other Organisms
RNA polymerase is also found in bacteria, archaea, and even some viruses. In bacteria, the enzyme consists of several subunits, and there is only one version. This version is initiated by a single transcription factor, called sigma. This protein first binds to the RNA polymerase, which is then more likely to bind to the correct promoter region. This method is slightly less efficient than the eukaryote method, in which there are many ways and proteins to inhibit or enhance gene expression.
Archaea have an RNA polymerase enzyme which is similar to both bacteria and eukaryotes, suggesting they are deeply related to both groups. While they only have 1 RNA polymerase type, it strongly represents both RNA polymerase II in eukaryotes as well as bacterial RNA.
Viruses, though they are not strictly considered living, also code for RNA polymerase, and include several unique types. Like living organisms, viruses have a need to express their DNA. Some viruses even have an RNA-dependent RNA polymerase. This is a confusing way of saying that the enzyme reads RNA to produce RNA. Unlike most organisms, some viruses store their genetic information as RNA, rather than DNA. These viruses must produce their own RNA polymerase because eukaryotic RNA polymerase would not be able to read RNA or express the viral genes. Some of these RNA polymerase enzymes are only a single subunit, being built from the smallest amount of genetic information possible.
RNA Polymerase and Evolution
This enzyme is strikingly similar among all the domains of life and is one of the reasons scientists suggest that all life originated from a common ancestor. RNA polymerase, as noted in the above section, creates a common debate among evolutionary scientists. Did genetic information start as RNA or DNA?
While it is simple to say that it must have been DNA because most life is now based on DNA, thinking about it may give you a headache. If DNA stores the information for RNA polymerase, but must be first decoded by RNA polymerase, how would the first DNA molecule have been replicated?
Without RNA polymerase, there is no mRNA and no proteins like polymerase itself. To fix this conundrum, scientists came up with the RNA world hypothesis. In this hypothesis, life started as simple strands of RNA. These strands of nucleotides would associate and dissociate at random, but certain combinations led to more stable patterns. Over time these chains gained the ability to be enzymes involved in binding amino acids, called ribozymes. These patterns of RNA are still seen in living organisms, as proof this is possible.
Eventually, as it is theorized, these ribozymes eventually evolved into fully housed protein complexes, what we would now call ribosomes. These structures have several pieces of RNA housed in a protein sheath. These complexes evolved over time to be extremely efficient at reproducing DNA and may have even created the first protocell. This fully housed RNA molecule system would be self-reproducing and may have been the first living cell.
The problem with the current theory, according to some scientists, is that it does not accurately reflect how DNA came into the picture. DNA, though still based on nucleotides, uses one different nucleotide and is a partially different system. However, these critics have a hard time explaining how DNA replicated itself. Some scientists suggest that DNA is a more structurally sound molecule, with a double-helix structure which protects it from damage. This could mean that some RNA organisms evolved DNA as a way of ensuring their genetic information would not be damaged. Others suggest that viruses may have introduced DNA into the RNA world.
Either way, RNA polymerase would have arisen as a natural means of decoding the DNA back into protein-producing RNA.