RNA polymerase

Team-2

RNA polymerase

Team Members:~

• Ishika Datta- A91704420085.

• Payal Guha- A91704420036.
• Nabanita Mazumder- A91704420044.
• Rohit Das- A91704420020.
• Pratyusha Mandal- A91704420056.
• Abhishek Jain- A91704420052.
• Adreeja Biswas- A91704420016.

Prokaryotic RNA Polymerase

• Core enzyme has the main function of reading the strand and synthesis of RNA
• Sigma factor only helps the core enzyme to attach them from promotor region to initiate reading process.
• RNA polymerase in prokaryotes. It is also named as RNA polymerase holoenzyme
• It is miltimeric enzyme consisting of two components –

1.core enzyme – 2 α , β β’ , ω 2. Sigma factor – σ factor

Prokaryotic RNA Polymerase

Role of Each Subunit:1. 2α – Determine the DNA to be transcribed 2. β - catalyze polymerasiation 3. β’ - Binds ans opens the template 4. ω - function not known 5. σ - Recognize the initiation sites called promoter

Eukaryotic RNA Polymerase

RNA Polymerase-1

RNA Polymerase-3

RNA Polymerase-2

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RNA polymerase I

Structure:

1. RNA Polymerase l is a 14-subunit enzyme that solely synthesizes pre-ribosomal RNA.. 2. It is a 14-subinut enzym that shares 5 subunits with Pol II and III(Rpb5, Rpb6, Rpb8, Rpb10, and Rpb12) that together with subunits A190, A135, AC40, AC19, and AC 12.2 form the core. Four additional subunits, the heterodimeric A43-A14 stalk, and the A49-A34.5 heterodimer complete the enzyme.

RNA polymerase I

Functions:

• RNA polymerase I is the structure where Ribosomal rna ( rRNA ) is synthesized by transcription and assembled into ribosomes.
• The rRNA are component elements of the ribosomes and are important in the process of translation
• Hence RNA polymerase 1 synthesizes almost all RNA except 5S rRNA

RNA polymerase II

Structure:

It is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. The 12 sub units of RNA polymerase are:-

• RPB7
• RPB8
• RPB9
• RPB10
• RPB11
• RPB12

• RPB1
• RPB2
• RPB3
• RPB4
• RPB5
• RPB6

https://doi.org/10.1016/B978-0-08-046884-6.00204-9

RNA polymerase II

Functions:

• RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells.
• Chromatin structure and histone posttranslational modification help regulate and record the transcription of genes by RNA polymerase II.
• Transcribes all protein-coding genes and many non-coding genes in eukaryotic genomes.

https://doi.org/10.1016/B978-0-08-046884-6.00204-9

RNA polymerase III

Structure:

• Pol III is a multi-subunit complex composed of 17 subunits.
• A central ten-subunit core, which harbors the catalytic site and a peripheral heterodimeric stalk that are structurally conserved among the three eukaryotic Pols.
• The structures revealed that the catalytic core of Pol III is similar to that of Pol I and Pol II, consistent with its conserved function in transcription elongation
• The TFIIF-like RPC4/5 and the TFIIE-like RPC3/6/7 subcomplexes are Pol III specific and can be regarded as built-in general transcription factors that play a fundamental role in Pol III transcription initiation and termination.

RNA polymerase III

Functions:

• RNA polymerase lll rely on a distinct set of proteins to initiate transcription.
• It also shares several identical core enzyme subunits with RNA polymerase II, they recognize very different promoter sequences and have unique general transcription factors.
• Pol III activity is highly regulated in a cell cycle and cell-type-dependent manner, and is a determinant of lifespan in eukaryotes.
• Although Pol III is best known for the nuclear transcription of small non-coding RNA genes, its function in the immune response is becoming increasingly clear.
• RNA Polymerase III Acts to Promote Organismal Aging.

RNA POLYMERASE-IV and V

Exclusively found in plants, RNA polymerase IV and V are transcription enzymes that evolved as specialized forms of RNA polymerase II. Both enzymes produce small interfering RNA (siRNA) transcripts, which play a role in the silencing of plant genes.

RNA POLYMERASE-IV and V

Function

• Plants encode extra RNA polymerases (Pol IV and V) that facilitate DNA methylation.
• Pol IV and V subunits evolved from Pol II subunits and are continuing to diversify.
• Pol IV and V differ in their composition and in the noncoding RNAs they produce.
• In vitro, Pol IV and V utilize non-canonical templates and require an RNA primer.
• Pol IV and V employ unique machinery to facilitate their recruitment to chromatin.

RNA-Dependent RNA Polymerase

Structure:

• Viral/prokaryotic RNA-directed RNA polymerases, along with many single-subunit DNA-directed polymerases, employ a fold whose organization has been linked to the shape of a right hand with three subdomains termed fingers, palm, and thumb.
• Only the palm subdomain, composed of a four-stranded antiparallel beta sheet with two alpha helices, is well conserved among all of these enzymes.

• Seven polymerase catalytic motifs are located in the RdRP palm and fingers domains, comprising the most conserved parts of the RdRP and are responsible for the RNA-only specificity in catalysis.
• In RdRp, the palm subdomain comprises three well-conserved motifs. Motif A and motif C are spatially juxtaposed; the aspartic acid residues of these motifs are implied in the binding of Mg2+ and/or Mn2+.

RNA-Dependent RNA Polymerase

Function:

• RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription.
• The RNA replication process is a four-step mechanism:

1. Nucleoside triphosphate (NTP) binding
2. Active site closure
3. Phosphodiester bond formation
4. Translocation

• RdRp differs from RNA polymerase as it works to catalyze the synthesis of an RNA strand complementary to a given RNA template, rather than using a DNA template.

Products of RNA Polymerase

Messenger RNA.

Ribosomal RNA.

Non-Coding RNA.

Micro RNA.

Catalytic RNA.

Transfer RNA.

De novo Synthesis by RNA Polymerase

RNAP accomplishes de novo synthesis. It is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers to start transcripts with ATP (followed by GTP, UTP, and then CTP). In contrast to DNA polymerase, RNAP includes helicase activity, therefore no separate enzyme is needed to unwind DNA.

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