RNA polymerase or Ribonucleic acid Polymerase (RNAP) enzyme is a multi-subunit enzyme whose main function is the catalyzation of the transcription process of RNA synthesized from a DNA sequence.
Due to that RNA polymerase is the enzyme that is responsible for the copying of DNA sequences into RNA sequences during transcription. As a complex molecule composed of protein subunits, RNA polymerase controls the process of transcription, during which the information stored in a molecule of DNA is copied into a new molecule of messenger RNA.
RNA polymerase has been found in all species, but the number and composition of these proteins vary across taxa. For example, bacteria contain a single type of RNA polymerase, while eukaryotes (multicellular and yeasts) contain three distinct types. In spite of these differences, these are striking similarities among transcription that can be regulated in order to achieve spatial and temporal changes in gene expression.
What is the role of RNA polymerase (RNAP)?
Generally, the RNAP molecule is a transcriptional molecule that plays an important role to transcribe information that is coded in DNA to synthesize protein in the cell cytoplasm. In the case of eukaryotes, before it starts protein, synthesis mRNA should get out from the cell nucleus to cytoplasm.
RNAP is playing a vital role in the synthesis of molecules that play a wide range of roles, out of that, one of its functions is to regulate the number and types of RNA synthesis in response to the requirement of the cell.
The RNA polymerase enzyme interacts with the different molecular proteins, transcription factors, and signaling molecules on the carboxyl-terminal. Which regulates its mechanisms, which play a vital role in gene expression and gene specialization in unicellular and multicellular organisms.
Because it controls the process of gene transcription that affects the patterns of gene expression and therefore, it allows the cell to adapt to a changing environment, perform a specialized role within an organism, and maintain basic metabolic processes necessary for the survival of the organism.
Therefore, it is not surprising that the activity of RNAP is long, complex, and highly regulated. In Escherichia coli bacteria, more than 100 transcription factors have been identified which modify the activity of RNAP.
RNAP first recognizes the specific sequence DNA sequence called a promoter and then gives a signal to initiate the process of transcription. And then produces an RNA chain, which is complementary to the template DNA strand. The process of adding nucleotides to the RNA strand Is known as elongation.
RNAP will preferentially release its RNA transcript then it reaches the termination sequence on the DNA templet which is encoded with the termination codon.
During transcription RNAP synthesize:
- mRNA which is acts as a templet for the protein-synthesizing by ribosomes.
- Noncoding RNA which is a broad class of gene that encode RNA that is not translated into protein.
- Such as Transfer RNA (tRNA) which is transferred specific amino acid to growing polypeptide chain at the ribosomal site if the protein synthesis during translation.
- Ribosomal RNA (rRNA) which is a component of the ribosomes
- Micro-RNA regulates the gene activity
- Catalytic RNA is enzymatically active RNA molecules.
The RNAP also ensures the irregularities and errors during the conversion of DNA to RNA (Transcription). Such as ensuring that the right ribonucleotide is added to the newly synthesized RNA strand, inserting the right amino acid-base which is complementary to the template DNA strand.
When the right nucleotide has been inserted, the RNA polymerase can then catalyze and elongate the RNA strand, at the same time, proofread the new strand and remove incorrect bases.
RNA polymerase is also involved in the post- transcription modification of RNAs in eukaryotes, converting them into functional molecules that facilitate the transcription of molecules from the nucleus to their site of action.
Some Other Function of RNA polymerase:
1) The RNAP Factory (in vitro)
Molecular motions of RNAP domains during transcription elongation have been addressed using a combination of site-directed mutagenesis and biochemical assays. Archaeal RNAP is highly amenable to factory analysis because, in some archaea, the two largest RNAP subunits found in eubacteria and eukarya are each divided into two polypeptide chains encoded by separated genes.
This allows more efficient assembly of these archaeal RNAPs from a recombinant protein produced in E. Coli, facilitating mutagenesis. Systematic substitution of the catalytic subunit of archaeal RNAP and subsequent high-throughput functional analyses of the mutation revealed flexible hinges in the bridge helix domain, which are important for transcription elongation.
2) Biophysics and translocation: RNA Polymerase as a motor and nanobot
Single-molecule studies provide unique insights into the dynamics and functioning of complex macromolecular machines. As reviewed by Michaelis and Treutlein, transcription initiation, elongation dynamics, effects of nucleosome packaging of the template, and possible consequences of transcription errors have been addressed using single-molecule approaches.
Details of the initiation and elongation complex architecture can be viewed using nanopositioning systems. Optical tweezers are employed to analyze RNAP elongation and encounter nucleosomes and terminators.
RNAP-nucleosome transactions have also been viewed by atomic force microscopy. Sophisticated probes of transcription initiation and elongation are developed for in vivo studies resulting in observation of transcriptional bursting, initiation, elongation, and factor recruitment and cycling.
Shimamoto considers RNAP as a complex nanoscale machine with diverse modes and functions. His review seeks to elucidate the biological roles of heterogeneity in RNAP locating a promoter, initiating transcription, and commencing elongation.
Investigations of molecular motions during transcription, including RNAP translocation, using single-molecule approaches are also discussed in his review. The energetics and kinetics of RNAP translocation via a thermal ratchet or a power stroke are compared.
The application of single-molecule techniques to understand heterogeneity in initiation and elongation complexes is discussed. Despite enthusiasm for new methods, caution is recommended in interpreting results from some single-molecule approaches including fluorescence resonance energy transfer.
3. Computational approaches
All-atom molecular dynamics simulation techniques and related approaches have been applied to multi-subunit RNAPs, reviewed by Wang et al. Because RNAP and DNAP mechanisms are so similar, both are considered.
Quantum methods to understand the core RNAP and DNAP mechanisms are discussed. Molecular dynamics is computationally expensive and has limitations in making and breaking covalent bonds. Quantum approaches potentially solve this problem but are limited to a small collection of selected atoms and are difficult to correlate with the experiment.
An interesting discussion of basic residues termed “histidine and arginine micro-switches” that may interact with the NTP, RNA, and DNA and drive conformational changes during each NAC is offered.