RNA polymerase- Definition, Types and Functions

RNA polymerase is a key enzyme that is essential for life. It is responsible for the synthesis of RNA molecules from DNA templates, a process known as transcription. Transcription is the first step in gene expression, which allows cells to produce proteins and perform various functions.

RNA polymerase is a complex molecule composed of several protein subunits that work together to catalyze the formation of RNA chains. Depending on the type of organism and the type of RNA being synthesized, different types of RNA polymerase may be involved. For example, bacteria have only one type of RNA polymerase that makes all kinds of RNA, while eukaryotes have at least three types of RNA polymerase that specialize in different classes of RNA.

RNA polymerase recognizes specific sequences of DNA called promoters that mark the beginning of a gene. It then unwinds the DNA strands and starts adding nucleotides that are complementary to the template strand of DNA. As it moves along the DNA, it elongates the RNA chain until it reaches a termination signal that tells it to stop and release the RNA product.

The RNA product may undergo further processing and modification before it becomes functional. For example, messenger RNA (mRNA) may be spliced, capped, and polyadenylated to form mature mRNA that can be translated into proteins by ribosomes. Other types of RNA, such as transfer RNA (tRNA), ribosomal RNA (rRNA), and small nuclear RNA (snRNA), may also undergo chemical modifications that affect their structure and function.

RNA polymerase is a highly regulated enzyme that responds to various signals and factors that influence its activity and specificity. For instance, transcription factors can bind to DNA or RNA polymerase and enhance or inhibit its initiation or elongation. Moreover, environmental stimuli, such as stress, hormones, or nutrients, can alter the expression of genes by affecting the availability or function of RNA polymerase.

In this article, we will explore the definition, types, and functions of RNA polymerase in more detail. We will also discuss how RNA polymerase plays a crucial role in protein synthesis and gene expression in different organisms.

RNA polymerase is an enzyme that catalyzes the synthesis of RNA from a DNA template. RNA polymerase uses the nucleotide sequence of one strand of DNA as a guide to assemble a complementary strand of RNA. The RNA strand that is produced is called the transcript, and it carries the genetic information from the DNA to other parts of the cell or to other cells.

RNA polymerase can be classified into different types based on the type of RNA that it synthesizes and the organism that it belongs to. For example, prokaryotes (such as bacteria and archaea) have a single type of RNA polymerase that synthesizes all kinds of RNA, while eukaryotes (such as animals, plants and fungi) have multiple types of RNA polymerase that specialize in synthesizing different kinds of RNA.

RNA polymerase is composed of several protein subunits that form a complex structure. The core subunits are responsible for the catalytic activity of the enzyme, while the accessory subunits are involved in the regulation and specificity of the transcription process. RNA polymerase also interacts with various factors and signals that modulate its function and expression.

RNA polymerase plays a crucial role in gene expression, which is the process by which the information encoded in DNA is converted into functional products such as proteins or RNAs. By controlling the rate and accuracy of transcription, RNA polymerase influences the amount and quality of the transcripts that are produced. RNA polymerase also participates in the post-transcriptional modification of RNAs, which involves adding or removing chemical groups or segments to alter their structure and function.

Transcription is the process of copying the DNA sequence of a gene into an RNA sequence, which can then be used for protein synthesis or gene regulation. Transcription is performed by a complex enzyme called RNA polymerase, which uses one strand of DNA as a template and synthesizes a complementary strand of RNA. The RNA strand that is produced by transcription is called the primary transcript, and it may undergo further processing before becoming functional.

RNA polymerase is composed of several protein subunits that work together to carry out the transcription process. The main steps of transcription are initiation, elongation, and termination. In each step, RNA polymerase interacts with different molecular factors that help it to recognize the correct DNA sequence, unwind the DNA helix, add nucleotides to the growing RNA chain, proofread the RNA sequence, and release the RNA transcript when it reaches the end of the gene.

Initiation

Initiation is the first step of transcription, in which RNA polymerase binds to a specific DNA sequence called the promoter, which marks the start of a gene. The promoter sequence varies depending on the type and location of the gene, but it usually contains a conserved region that is recognized by a subunit of RNA polymerase called sigma factor . The sigma factor helps RNA polymerase to bind to the promoter with high specificity and affinity . Once bound, RNA polymerase separates the two strands of DNA near the promoter region, creating a transcription bubble where the template strand is exposed .

Elongation

Elongation is the second step of transcription, in which RNA polymerase moves along the template strand and adds nucleotides to the 3` end of the growing RNA chain . The nucleotides are complementary to the template strand, meaning that adenine (A) pairs with thymine (T), cytosine (C) pairs with guanine (G), and uracil (U) pairs with adenine (A) in RNA . The direction of synthesis is 5` to 3`, meaning that the new nucleotides are added to the 5` end of the incoming nucleotide and to the 3` end of the previous nucleotide . As RNA polymerase moves along the DNA, it unwinds the helix ahead of it and rewinds it behind it, maintaining a constant size of the transcription bubble .

Termination

Termination is the final step of transcription, in which RNA polymerase stops adding nucleotides and releases the RNA transcript from the DNA template . Termination can occur in different ways depending on the type and organism of the gene. In bacteria, termination can be either rho-dependent or rho-independent . Rho-dependent termination involves a protein factor called rho that binds to a specific sequence on the RNA transcript and moves along it until it reaches RNA polymerase, causing it to dissociate from the DNA . Rho-independent termination involves a sequence on the RNA transcript that forms a hairpin loop structure that destabilizes the interaction between RNA polymerase and DNA . In eukaryotes, termination can involve different mechanisms such as polyadenylation signals, cleavage factors, or termination factors .

Summary

RNA polymerase is an enzyme that catalyzes the synthesis of RNA from a DNA template during transcription. It has three main steps: initiation, elongation, and termination. In each step, it interacts with different molecular factors that regulate its activity and ensure its fidelity. Transcription is essential for gene expression and protein synthesis in all living organisms.

RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of 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 polymerases have been found in all species, but the number and composition of these proteins vary across taxa. For instance, bacteria contain a single type of RNA polymerase, while eukaryotes (multicellular organisms and yeasts) contain three distinct types. In spite of these differences, there are striking similarities among transcriptional mechanisms. For example, all species require a mechanism by which transcription can be regulated in order to achieve spatial and temporal changes in gene expression.

Prokaryotic RNA polymerase

The prokaryotes (bacteria, viruses, archaea) have a single type of RNA polymerase (RNAP) which synthesizes all the classes of RNA, i.e mRNA, tRNA, rRNA, sRNA. The RNA Polymerase molecule is made up of two domains and five subunits:

• Core and holoenzyme
• Subunits (β, β’, α (αI and αII), ω)

The core enzyme consists of four subunits: β, β’, and two copies of α. The core enzyme can synthesize RNA but cannot initiate transcription accurately. The holoenzyme is formed when a sigma (σ) factor binds to the core enzyme. The sigma factor confers specificity to the holoenzyme by recognizing specific promoter sequences on the DNA template.

The promoter is the sequence of DNA that is required for accurate and specific initiation of transcription, and also, it is the sequence of DNA to which RNA polymerase binds accurately to initiate transcription. The ‘α’ subunit is made up of two distinct domains. The N-terminal domain (α-NTD) and the C-terminal domain (α-CTD). The N-terminal domain is involved in dimerization forming α2 and further assembly of the RNA polymerase. The C-terminal domain functions such as binding to the Upstream Promoter (UP) DNA sequence at promoters for rRNA and tRNA genes and in communication with several transcriptional activators.

Eukaryotic RNA polymerase

There are five known types of RNA polymerases each responsible for the synthesis of specific subtypes of RNA. These include:

• RNA polymerase I that synthesizes a pre-rRNA 45S (35S in yeast), which matures and forms the major RNA sections of the ribosome.
• RNA polymerase II synthesizes precursors of mRNAs and most snRNA and microRNAs.
• RNA polymerase III synthesizes tRNAs, rRNA 5S, and other small RNAs found in the nucleus and cytosol.
• RNA polymerase IV and V found in plants are not well understood, however, they make siRNA. The plant chloroplast encodes the ssRNAPs and uses bacteria-like RNA Polymerase.

Each of the nuclear RNA polymerases is a large protein molecule with about 8 to 14 subunits and the molecular weight is approximately 500,000 for each. They commonly have three subunits, α, β and β’. The largest subunits being β and β’. These subunits are used as catalytic promoters and for assembly of proteins.

Each of these polymerases has a different function:

• RNA polymerase I that synthesizes a pre-rRNA 45S (35S in yeast), which matures and forms the major RNA sections of the ribosome.
• RNA polymerase II synthesizes precursors of mRNAs and most snRNA and microRNAs.
• RNA polymerase III synthesizes tRNAs, rRNA 5S, and other small RNAs found in the nucleus and cytosol.
• RNA polymerases IV and V found in plants are not well understood, however, they make siRNA. The plant chloroplast encodes the ssRNAPs and uses bacteria-like RNA Polymerase.

The prokaryotes have a single type of RNA polymerase (RNAP) which synthesizes all the classes of RNA, i.e mRNA, tRNA, rRNA, sRNA. The RNA Polymerase molecule is made up of two domains and five subunits:

• The core domain consists of four subunits: β, β`, α (αI and αII), and ω. The core domain is responsible for the catalytic activity of the enzyme and the elongation of the RNA chain.
• The σ domain consists of a single subunit: σ. The σ subunit is responsible for the recognition and binding of the promoter sequence on the DNA template. The σ subunit also confers specificity to the enzyme, as different σ factors can recognize different promoters.

The core domain and the σ subunit together form the holoenzyme, which is the active form of the RNAP. The holoenzyme initiates transcription by unwinding a short region of the DNA template and synthesizing a short RNA primer. The holoenzyme then releases the σ subunit and continues to elongate the RNA chain until it reaches a termination signal on the DNA template.

The prokaryotic RNAP can be regulated by various factors, such as:

• Transcription factors: These are proteins that bind to specific DNA sequences and either enhance or inhibit the binding of RNAP to the promoter. For example, catabolite activator protein (CAP) binds to promoters of genes involved in sugar metabolism and activates their transcription in response to low glucose levels.
• Sigma factors: These are proteins that bind to the core domain of RNAP and alter its promoter specificity. For example, σ^70^ is the most common sigma factor in E. coli and recognizes most of the housekeeping genes. However, under stress conditions, such as heat shock or starvation, alternative sigma factors, such as σ^32^ or σ^54^, are expressed and recognize different promoters that encode for stress response genes.
• Anti-sigma factors: These are proteins that bind to sigma factors and prevent them from associating with the core domain of RNAP. For example, Rsd binds to σ^70^ and inhibits its activity in E. coli.
• Small RNAs: These are short non-coding RNAs that regulate gene expression by base-pairing with target mRNAs and either enhancing or inhibiting their translation or stability. For example, DsrA is a small RNA that activates the expression of RpoS, an alternative sigma factor that controls the general stress response in E. coli.

The prokaryotic RNAP is a versatile and adaptable enzyme that can synthesize all types of RNA molecules in response to various environmental signals and cellular needs.

Eukaryotes are organisms that have a membrane-bound nucleus and other organelles in their cells. Unlike prokaryotes, which have a single type of RNA polymerase, eukaryotes have multiple types of RNA polymerases that are specialized for different functions. These include:

• RNA polymerase I, which synthesizes the precursor of the large ribosomal RNA (rRNA) molecules. These rRNAs form the core of the ribosomes, which are the sites of protein synthesis in the cell. RNA polymerase I is located in the nucleolus, a specialized region of the nucleus where rRNA transcription and ribosome assembly occur.
• RNA polymerase II, which synthesizes the precursors of messenger RNA (mRNA) and some small nuclear RNA (snRNA) and microRNA (miRNA) molecules. These RNAs are involved in various aspects of gene expression, such as transcription regulation, splicing, translation, and degradation. RNA polymerase II is located in the nucleoplasm, the main part of the nucleus where most of the DNA is found.
• RNA polymerase III, which synthesizes the precursors of transfer RNA (tRNA) and some small nucleolar RNA (snoRNA) and small cytoplasmic RNA (scRNA) molecules. These RNAs are essential for protein synthesis and modification, as they carry amino acids to the ribosomes and guide the chemical modification of rRNAs. RNA polymerase III is also located in the nucleoplasm.
• RNA polymerases IV and V, which are found only in plants and are involved in the production of small interfering RNA (siRNA) molecules. These RNAs play a role in gene silencing and heterochromatin formation, which are processes that regulate gene expression by preventing transcription or translation of certain genes. RNA polymerases IV and V are located in the nucleus but their exact localization is not clear.

Each type of eukaryotic RNA polymerase has a distinct structure and composition, consisting of several protein subunits that form a complex. Some subunits are common to all types of RNA polymerases, while others are specific to each type. The common subunits are called core subunits and they form the catalytic center of the enzyme, where the synthesis of RNA takes place. The specific subunits are called accessory subunits and they confer specificity and regulation to each type of RNA polymerase.

Eukaryotic RNA polymerases also require additional factors to initiate and regulate transcription. These factors include transcription factors, which bind to specific DNA sequences called promoters and recruit RNA polymerases to start transcription; enhancers and silencers, which modulate transcription by interacting with transcription factors; mediators, which mediate the communication between transcription factors and RNA polymerases; and chromatin modifiers, which alter the structure and accessibility of DNA by adding or removing chemical groups.

Eukaryotic RNA polymerases are highly regulated by various mechanisms that ensure proper gene expression in response to internal and external signals. Some of these mechanisms include:

• Transcription initiation, which determines when and where transcription starts by controlling the assembly of the pre-initiation complex (PIC), a large protein complex that includes RNA polymerase and other factors.
• Transcription elongation, which determines how fast and accurate transcription proceeds by controlling the movement and stability of RNA polymerase along the DNA template.
• Transcription termination, which determines when and how transcription ends by controlling the release of RNA polymerase and the newly synthesized RNA from the DNA template.
• Transcription coupling, which coordinates transcription with other processes such as DNA replication, repair, recombination, and chromatin remodeling.
• Post-transcriptional processing, which modifies the newly synthesized RNAs by adding or removing segments or chemical groups to generate functional RNAs.

Eukaryotic RNA polymerases are essential for life, as they produce a variety of RNAs that perform diverse functions in the cell. They also play a key role in gene expression regulation, which allows eukaryotes to adapt to changing environments and maintain cellular homeostasis.

RNA polymerase I (RNAP I) is the enzyme that synthesizes a pre-rRNA 45S (35S in yeast), which matures and forms the major RNA sections of the ribosome. The ribosome is the molecular machine that translates mRNA into proteins. Therefore, RNAP I is essential for protein synthesis and cell growth.

RNAP I is located in the nucleolus, a specialized nuclear substructure where rRNA transcription and ribosome assembly take place. The nucleolus is formed around clusters of rRNA genes, called ribosomal DNA (rDNA), which are repeated hundreds of times in the genome. Each rDNA repeat contains a promoter, a transcribed region, and an intergenic spacer.

RNAP I consists of 14 subunits in humans, 13 subunits in yeast, and 10 subunits in archaea. The core enzyme shares some common subunits with RNAP II and III, but also has unique subunits that confer specificity and regulation. The largest subunit, RPA1, contains a C-terminal domain (CTD) that interacts with various factors involved in transcription initiation, elongation, termination, and processing.

RNAP I transcription is tightly regulated by both external and internal signals, such as nutrient availability, stress response, cell cycle, and growth factors. The regulation occurs at multiple levels, including chromatin remodeling, rDNA copy number, promoter selection, transcription factor binding, and post-translational modifications. Dysregulation of RNAP I transcription can lead to diseases such as cancer and aging-related disorders.

The main steps of RNAP I transcription are:

• Initiation: RNAP I binds to the promoter region of rDNA with the help of several transcription factors, such as UBF (upstream binding factor), SL1 (selectivity factor 1), and TIF-IA (transcription initiation factor IA). These factors form a pre-initiation complex (PIC) that positions RNAP I at the transcription start site and unwinds the DNA.
• Elongation: RNAP I moves along the rDNA template and synthesizes a long pre-rRNA molecule. The elongation process is facilitated by several factors, such as TIF-IB (transcription elongation factor IB), SPT4/5 (suppressor of Ty 4/5), and FACT (facilitates chromatin transcription). These factors help RNAP I overcome obstacles such as nucleosomes, DNA damage, and secondary structures.
• Termination: RNAP I stops transcription when it reaches a terminator sequence in the rDNA intergenic spacer. The termination process involves several factors, such as TTF-I (termination factor I), PTRF (polymerase I transcription release factor), and RENT (regulator of nucleolar silencing and telophase exit) complex. These factors induce RNAP I to pause, release the pre-rRNA transcript, and dissociate from the DNA template.
• Processing: The pre-rRNA transcript undergoes extensive processing steps to generate mature rRNAs. The processing steps include cleavage, trimming, modification, and assembly with ribosomal proteins. The processing factors are mostly located in the nucleolus and include snoRNPs (small nucleolar ribonucleoproteins), exosomes, endonucleases, methyltransferases, and pseudouridine synthases.

The final products of RNAP I transcription are three major rRNAs: 18S rRNA (part of the small ribosomal subunit), 28S rRNA and 5.8S rRNA (part of the large ribosomal subunit). These rRNAs are exported to the cytoplasm and join with the 5S rRNA (synthesized by RNAP III) to form functional ribosomes.

RNA polymerase II (RNAP II) is the enzyme that synthesizes precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA (miRNA) in eukaryotic cells. These RNAs are involved in protein synthesis and gene regulation.

RNAP II is located in the nucleus and consists of 12 subunits with a total mass of about 550 kDa. The largest subunits are Rpb1 and Rpb2, which contain the catalytic center and bind to the DNA template. The other subunits have various roles in transcription initiation, elongation, termination, and processing.

RNAP II recognizes specific DNA sequences called promoters, which are located upstream of the transcription start site. Promoters usually contain a TATA box, a short sequence of nucleotides that is recognized by a protein called TATA-binding protein (TBP), which is part of a complex called TFIID. TFIID recruits other transcription factors (TFIIB, TFIIE, TFIIF, and TFIIH) that form the pre-initiation complex (PIC) with RNAP II. The PIC unwinds the DNA and positions RNAP II at the start site.

RNAP II then begins to synthesize RNA from the DNA template in the 5` to 3` direction, using ribonucleoside triphosphates as substrates. The first nucleotide added is usually a purine (adenine or guanine), which forms a cap structure at the 5` end of the RNA. The cap protects the RNA from degradation and facilitates its export from the nucleus and its recognition by the ribosome.

As RNAP II elongates the RNA chain, it encounters various signals that regulate its activity. For example, some DNA sequences can cause RNAP II to pause or stall, allowing for the recruitment of other factors that modulate transcription or process the RNA. One such factor is P-TEFb, which phosphorylates the C-terminal domain (CTD) of Rpb1, a long and repetitive sequence of amino acids that protrudes from the enzyme. The phosphorylation of the CTD enhances the elongation rate and also serves as a platform for the binding of other proteins that modify or splice the RNA.

RNAP II terminates transcription when it reaches a polyadenylation signal (usually AAUAAA) in the DNA template, which triggers the cleavage of the RNA and the addition of a poly(A) tail at its 3` end. The poly(A) tail stabilizes the RNA and promotes its translation by the ribosome. The released RNAP II can then be recycled for another round of transcription.

RNAP II is regulated by various mechanisms that ensure proper gene expression in response to cellular signals and environmental stimuli. For example, some transcription factors can activate or repress RNAP II binding to specific promoters by interacting with coactivators or corepressors. Some chromatin modifications, such as histone acetylation or methylation, can also affect RNAP II accessibility to DNA by altering its structure. Moreover, some non-coding RNAs, such as miRNAs or long non-coding RNAs (lncRNAs), can modulate RNAP II activity by binding to its transcripts or influencing its localization.

RNAP II is essential for eukaryotic gene expression and plays a key role in many biological processes, such as development, differentiation, cell cycle, apoptosis, stress response, and disease. Mutations or dysregulation of RNAP II or its associated factors can lead to various disorders, such as cancer, neurodegeneration, inflammation, and viral infection.

RNA polymerase III (Pol III) is located in the nucleus and is responsible for transcribing various types of small RNAs, such as transfer RNA (tRNA), 5S ribosomal RNA (rRNA), and U6 small nuclear RNA (snRNA). These RNAs are essential for protein synthesis and splicing. The genes transcribed by Pol III are considered "housekeeping" genes, as they are required in all cell types and most environmental conditions. However, Pol III activity can also be regulated by various factors, such as cell growth, stress, and signaling molecules.

Pol III has a complex structure composed of 17 subunits, some of which are shared with other polymerases and some of which are specific to Pol III. The core subunits include two large subunits (RPC1 and RPC2) that form the catalytic center, two stalk subunits (RPC10 and RPC11) that interact with transcription factors, and six common subunits (RPABC1-6) that are also found in Pol I and Pol II. The specific subunits include a TFIIF-like heterodimer (RPC4 and RPC5), a TFIIE-like heterodimer (RPC3 and RPC6), a TFIIE-like monomer (RPC7), and a zinc finger protein (RPC8).

Pol III initiation requires the assembly of a pre-initiation complex (PIC) on the promoter region of the gene. The promoter can be either internal or external to the transcribed sequence, depending on the type of gene. There are three classes of Pol III promoters: type 1, type 2, and type 3. Type 1 promoters are found in 5S rRNA genes and consist of three internal elements: A block, C block, and intermediate element. Type 2 promoters are found in tRNA genes and consist of two internal elements: A box and B box. Type 3 promoters are found in U6 snRNA genes and consist of an external TATA box and a proximal sequence element.

The PIC formation involves the sequential binding of several transcription factors to the promoter elements. The first factor to bind is TFIIIA for type 1 promoters or TFIIIC for type 2 and type 3 promoters. TFIIIA and TFIIIC serve as scaffolds for the recruitment of TFIIIB, which consists of three subunits: TATA-binding protein (TBP), B-related factor (BRF1 or BRF2), and B-double prime (BDP1). TFIIIB binds to the TATA box or the A box and recruits Pol III to the promoter. The PIC is then stabilized by the interaction of Pol III with TFIIIC and other factors, such as SNAPc for type 3 promoters. The PIC is also modified by various co-factors that regulate Pol III activity, such as Maf1, TOR, Rapamycin, and others.

Once the PIC is formed, Pol III starts to unwind the DNA template and synthesize the RNA transcript in the 5` to 3` direction. The elongation process is highly processive and accurate, as Pol III has intrinsic proofreading and editing mechanisms. The termination process depends on the type of gene transcribed. For type 1 genes, Pol III terminates after transcribing a terminator element that forms a stem-loop structure followed by a run of uracils. For type 2 genes, Pol III terminates after adding a few extra nucleotides beyond the mature end of the tRNA transcript. For type 3 genes, Pol III terminates after encountering a poly-T tract that causes pausing and release of the transcript. After termination, Pol III dissociates from the DNA template and can re-initiate transcription on another promoter.

RNA polymerases IV and V are two types of RNA polymerases that are found only in plants. They are closely related to RNA polymerase II in terms of structure and subunit composition, but they have distinct functions and localization in the cell nucleus.

RNA polymerase IV (RNAP IV) is involved in the production of small interfering RNAs (siRNAs) that mediate RNA interference (RNAi), a process that silences gene expression by degrading or inhibiting the translation of target RNAs. RNAP IV transcribes non-coding regions of the genome, such as transposable elements, repetitive sequences, and intergenic regions, generating long non-coding RNAs (lncRNAs) that are processed into siRNAs by the DICER-LIKE 3 (DCL3) enzyme. These siRNAs are then loaded onto ARGONAUTE 4 (AGO4) proteins and guide them to complementary target RNAs for silencing.

RNA polymerase V (RNAP V) is also involved in RNAi, but it acts downstream of RNAP IV and siRNAs. RNAP V transcribes specific regions of the genome that are marked by histone modifications or DNA methylation, generating lncRNAs that are processed into siRNAs by DCL2 and DCL4 enzymes. These siRNAs are then loaded onto AGO6 or AGO9 proteins and guide them to complementary target RNAs for silencing. In addition, RNAP V also interacts with chromatin-remodeling complexes and histone-modifying enzymes to establish and maintain heterochromatin, a condensed form of chromatin that represses gene expression.

RNA polymerases IV and V are essential for plant development and stress responses, as they regulate the expression of genes involved in various biological processes, such as flowering, seed development, defense against pathogens, and adaptation to environmental changes. They also play a role in maintaining genome stability and preventing the activation of transposable elements that can cause mutations or rearrangements.

The following table summarizes the main features of RNA polymerases IV and V:

RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of 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 polymerases have been found in all species, but the number and composition of these proteins vary across taxa. For instance, bacteria contain a single type of RNA polymerase, while eukaryotes (multicellular organisms and yeasts) contain three distinct types. In spite of these differences, there are striking similarities among transcriptional mechanisms. For example, all species require a mechanism by which transcription can be regulated in order to achieve spatial and temporal changes in gene expression.

RNA polymerase has several functions that are essential for life:

• It synthesizes different types of RNA molecules that play a wide range of roles in the cell. These include:

  • Messenger RNA (mRNA), which carries the genetic code for protein synthesis from the nucleus to the cytoplasm.
  • Transfer RNA (tRNA), which transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation.
  • Ribosomal RNA (rRNA), which incorporates into ribosomes and forms the site of protein synthesis.
  • Small nuclear RNA (snRNA), which participates in the processing and splicing of pre-mRNA.
  • Micro RNA (miRNA), which regulates gene expression by binding to complementary sequences on mRNA and inhibiting translation or promoting degradation.
  • Small interfering RNA (siRNA), which mediates RNA interference, a process that silences gene expression by targeting specific mRNA molecules for degradation.
  • Catalytic RNA (ribozyme), which functions as an enzymatically active RNA molecule that can catalyze chemical reactions.

• It interacts with different molecular proteins, transcription factors, and signaling molecules that regulate its activity and specificity. These include:

  • Promoter sequences, which are DNA regions that bind to RNA polymerase and initiate transcription.
  • Transcription factors, which are proteins that bind to specific DNA sequences and modulate the rate and efficiency of transcription.
  • Mediator complex, which is a large protein complex that bridges RNA polymerase II and various transcription factors and coactivators.
  • Sigma factor, which is a protein that associates with bacterial RNA polymerase and confers promoter recognition and specificity.

• It ensures fidelity and accuracy during the transcription process. This involves:

  • Selecting the correct nucleotide to be added to the growing RNA strand based on the complementary base pairing with the DNA template.
  • Proofreading and removing incorrect nucleotides from the RNA strand using its intrinsic exonuclease activity.
  • Pausing and terminating transcription at specific signals or sequences on the DNA template.

• It performs post-transcriptional modifications on some RNA molecules to make them functional. These include:

  • Capping, which is the addition of a modified guanine nucleotide at the 5` end of mRNA to protect it from degradation and facilitate translation initiation.
  • Polyadenylation, which is the addition of a poly-A tail at the 3` end of mRNA to increase its stability and export from the nucleus.
  • Splicing, which is the removal of introns (non-coding regions) and joining of exons (coding regions) in pre-mRNA to produce mature mRNA.
  • Editing, which is the alteration of nucleotides in some RNA molecules to change their coding or regulatory potential.

In summary, RNA polymerase is a vital enzyme that performs multiple functions in the cell related to transcription, gene expression, and protein synthesis. It is involved in the synthesis of various types of RNA molecules that have different roles and functions in the cell. It also interacts with various proteins and factors that regulate its activity and specificity. It ensures fidelity and accuracy during transcription by selecting, proofreading, and removing nucleotides. It also performs post-transcriptional modifications on some RNA molecules to make them functional.

RNA plays a crucial role in protein synthesis and gene expression. Protein synthesis is the process by which the information stored in DNA is translated into amino acid sequences that form the building blocks of proteins. Gene expression is the process by which genes are activated or silenced to produce specific proteins that determine the traits and functions of cells.

Protein synthesis

Protein synthesis involves two main steps: transcription and translation. Transcription is the process by which a DNA sequence of a gene is copied into a complementary RNA sequence. Translation is the process by which the RNA sequence is decoded into a specific amino acid sequence that forms a polypeptide chain.

Three types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

• mRNA carries the genetic code from DNA to the ribosomes, which are the sites of protein synthesis in the cytoplasm. Each mRNA molecule contains a series of codons, which are three-nucleotide sequences that correspond to specific amino acids or stop signals.
• tRNA carries the appropriate amino acids to the ribosomes during translation. Each tRNA molecule has an anticodon, which is a three-nucleotide sequence that is complementary to a codon on the mRNA. The tRNA also has an attachment site for the amino acid that matches the codon.
• rRNA forms the core of the ribosomes and catalyzes the formation of peptide bonds between adjacent amino acids on the polypeptide chain. rRNA also ensures that the mRNA, tRNA, and ribosomes are properly aligned during translation.

Gene expression

Gene expression is regulated by various factors, such as transcription factors, signaling molecules, and non-coding RNAs. Non-coding RNAs are RNA molecules that do not encode proteins but have other functions in the cell. Some examples of non-coding RNAs are:

• Small regulatory RNAs (sRNAs), such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), that modulate gene expression by binding to complementary sequences on mRNA and either blocking translation or promoting degradation.
• Long non-coding RNAs (lncRNAs), such as X-inactive specific transcript (XIST) and Hox transcript antisense intergenic RNA (HOTAIR), that regulate gene expression by interacting with chromatin, transcription factors, or other RNAs and affecting their activity or stability.
• Catalytic RNAs (ribozymes), such as ribonuclease P (RNase P) and hammerhead ribozyme, that perform biochemical reactions by cleaving or joining other RNA molecules.

Non-coding RNAs play important roles in various biological processes, such as development, differentiation, cell cycle, apoptosis, immunity, and stress response. They also contribute to various diseases, such as cancer, neurodegeneration, and viral infections.

In summary, RNA is essential for protein synthesis and gene expression in cells. RNA molecules carry out diverse functions by interacting with DNA, proteins, or other RNAs through complementary base pairing or enzymatic activity.

After RNA polymerase synthesizes a primary transcript of RNA from a DNA template, the RNA molecule undergoes various modifications before it becomes functional. These modifications are collectively known as post-transcriptional modifications and they occur in both prokaryotes and eukaryotes.

Some of the common post-transcriptional modifications are:

• Capping: This is the addition of a 7-methylguanosine cap to the 5` end of the RNA molecule. This cap protects the RNA from degradation by exonucleases and facilitates its transport out of the nucleus. It also helps in the initiation of translation by binding to the cap-binding complex of the ribosome. Capping is catalyzed by a capping enzyme that associates with RNA polymerase II in eukaryotes.
• Polyadenylation: This is the addition of a poly(A) tail, which consists of a series of adenine nucleotides, to the 3` end of the RNA molecule. This tail enhances the stability and lifespan of the RNA and aids in its export from the nucleus. It also plays a role in termination of transcription by RNA polymerase II in eukaryotes. Polyadenylation is catalyzed by a poly(A) polymerase that is recruited by a cleavage and polyadenylation specificity factor (CPSF) that binds to a polyadenylation signal sequence on the RNA.
• Splicing: This is the removal of introns, which are non-coding regions of the RNA, and the joining of exons, which are coding regions of the RNA. This process generates mature mRNA molecules that encode for proteins. Splicing is carried out by a complex of proteins and small nuclear RNAs (snRNAs) called the spliceosome, which recognizes splice sites on the RNA and catalyzes the splicing reaction. Splicing can also occur in some tRNAs and rRNAs.
• Editing: This is the alteration of one or more nucleotides in the RNA molecule by insertion, deletion, or substitution. This process can change the coding or regulatory information of the RNA and affect its function. Editing can be mediated by enzymes or guide RNAs (gRNAs) that recognize specific sequences on the RNA and direct the editing reaction. Editing occurs in some mRNAs, tRNAs, rRNAs, and microRNAs.

These post-transcriptional modifications are essential for generating functional RNAs that participate in various cellular processes such as protein synthesis and gene expression. RNA polymerase is involved in these modifications either directly or indirectly by interacting with other factors that perform these modifications. By regulating these modifications, RNA polymerase can control the quality and quantity of RNAs in the cell.

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