RNA polymerase

Examples of RNA polymerase in the following topics:

• Elongation and Termination in Eukaryotes

  • RNA Polymerase II will continue to elongate the newly-synthesized RNA until transcription terminates.
  • RNA Polymerase II is a complex of 12 protein subunits.
  • The tRNA, 5S rRNA, and structural RNAs genes transcribed by RNA Polymerase III have a not-entirely-understood termination signal.
  • The RNAs transcribed by RNA Polymerase III have a short stretch of four to seven U's at their 3' end.
  • Xrn2 will start digesting the non-released portion of the newly synthesized RNA until Xrn2 reaches the RNA Polymerase, where it aids in displacing the RNA Polymerase from the template DNA strand.

• Initiation of Transcription in Eukaryotes

  • RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule.
  • RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs.
  • RNA polymerase III is also located in the nucleus.
  • This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs.
  • Not all miRNAs are transcribed by RNA Polymerase II, RNA Polymerase III transcribes some of them.

• The Promoter and the Transcription Machinery

  • RNA polymerase binds to the transcription initiation complex, allowing transcription to occur.
  • Once this transcription initiation complex is assembled, RNA polymerase can bind to its upstream sequence.
  • When bound along with the transcription factors, RNA polymerase is phosphorylated.
  • A generalized promoter of a gene transcribed by RNA polymerase II is shown.
  • RNA polymerase II then binds and forms the transcription initiation complex.

• Initiation of Transcription in Prokaryotes

  • Prokaryotes use the same RNA polymerase to transcribe all of their genes.
  • Each subunit has a unique role: the two α-subunits are necessary to assemble the polymerase on the DNA; the β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent "recently-born" mRNA molecule; and the β' binds the DNA template strand.
  • It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site.
  • The polymerase comprised of all five subunits is called the holoenzyme.
  • The σ subunit of prokaryotic RNA polymerase recognizes consensus sequences found in the promoter region upstream of the transcription start sight.

• Elongation and Termination in Prokaryotes

  • The dissociation of σ allows the core RNA polymerase enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second.
  • Since the base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components, RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.
  • Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain.
  • This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.
  • During elongation, the prokaryotic RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5' to 3' direction, and unwinds and rewinds the DNA as it is read.

• Viral Replication and Gene Expression

  • Viruses that replicate via RNA intermediates need an RNA-dependent RNA-polymerase to replicate their RNA, but animal cells do not seem to possess a suitable enzyme.
  • Therefore, this type of animal RNA virus needs to code for an RNA-dependent RNA polymerase.
  • No viral proteins can be made until viral messenger RNA is available; thus, the nature of the RNA in the virion affects the strategy of the virus: In plus-stranded RNA viruses, the virion (genomic) RNA is the same sense as mRNA and so functions as mRNA.
  • One of these includes RNA-dependent RNA polymerase (RNA replicase), which copies the viral RNA to form a double-stranded replicative form, in turn this directs the formation of new virions.
  • The positive-sense RNA serves as template for complementary negative-strand synthesis, thereby producing a double-stranded RNA (replicative form, RF) (5).

• Positive-Strand RNA Viruses of Animals

  • Positive strand RNA viruses are the single largest group of RNA viruses with 30 families.
  • Single stranded RNA viruses can be classified according to the sense or polarity of their RNA into negative-sense and positive-sense, or ambisense RNA viruses.
  • Positive-sense viral RNA is similar to mRNA and thus can be immediately translated by the host cell.
  • Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation.
  • The genome RNA is unusual because it has a protein on the 5' end that is used as a primer for transcription by RNA polymerase.

• mRNA Processing

  • While RNA Polymerase II is still transcribing downstream of the proper end of a gene, the pre-mRNA is cleaved by an endonuclease-containing protein complex between an AAUAAA consensus sequence and a GU-rich sequence.
  • This releases the functional pre-mRNA from the rest of the transcript, which is still attached to the RNA Polymerase.
  • An enzyme called poly (A) polymerase (PAP) is part of the same protein complex that cleaves the pre-mRNA and it immediately adds a string of approximately 200 A nucleotides, called the poly (A) tail, to the 3' end of the just-cleaved pre-mRNA.
  • Poly (A) Polymerase adds a 3' poly (A) tail to the pre-mRNA.
  • The pre-mRNA is cleaved off the rest of the growing transcript before RNA Polymerase II has stopped transcribing.

• The Protein Synthesis Machinery

  • Protein synthesis, or translation of mRNA into protein, occurs with the help of ribosomes, tRNAs, and aminoacyl tRNA synthetases.
  • The tRNA molecules are transcribed by RNA polymerase III.
  • The transfer RNAs (tRNAs) are structural RNA molecules.
  • In eukaryotes, tRNA mole are transcribed from tRNA genes by RNA polymerase III.
  • The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule.

• Small Regulatory RNAs

  • Small regulatory RNAs encompass a specific class of RNAs that affect gene regulation.
  • Antisense RNAs are used to bind to complementary mRNAs and inhibit protein translation.
  • The antisense RNAs are categorized as small regulatory RNAs due to their small size.
  • House-keeping RNAs identified to date include rRNA and tRNAs. rRNAs that are considered to be house-keeping genes can bind to RNA polymerases and regulate transcription or function in larger complexes that are required for protein secretion or synthesis processes.
  • The antisense RNA can bind to the mRNA and inhibit translation.