User:Jordan Scott/Sandbox RNA polII: Difference between revisions
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RNAP II is responsible for the synthesis of pre-mRNA and | RNAP II is responsible for the synthesis of pre-mRNA and snRNAs. It is 550 kDa and made of 12 subunits (Rpb1-12) that range from 220-10 kDa. The subunits are highly conserved to the point that mammalian subunits can substitute with yeast subunits are there are little to no defects.(B0) There are two large sub units and 10 smaller subunits, some of which are shared with RNAPs I and III. The active site of RNAP II is mostly made of the the two largest subunits Rpb1 and Rpb2. | ||
Rpb1 also has a CTD that contains heptad repeats of YSPTSPS.(G) This region serves as the main control point for RNAP II. The CTD experiences various conformation changes based on it being in a hypo or hyper phosphorylation state. The heptad repeats may also exist in several forms with one repeat having 16 known states. These states form a CTD code that is used to regulate the various stages of transcription and mRNA processing. The CTD is also shown to a part of cell cycle regulation as CDK/cyclins involved in the cell cycle modify the CTD and coordinate gene expression. (G) | |||
While RNAP II is capable of transcription by itself it is non-selective of any particular DNA region. However some mutageneis studies have shown that RNAP II may have some role in selectivity. (A) To properly recognize regions upstream of the gene's transcription start site it requires several general transcription factors that are selective for these regions known as promoters and positions RNAP to accurately begin transcription. (B) These GTF's and other accessory proteins called SRBs are necessary for accurate transcription and together with the RNAP II core enzyme form the RNAP holoenzyme. | While RNAP II is capable of transcription by itself it is non-selective of any particular DNA region. However some mutageneis studies have shown that RNAP II may have some role in selectivity. (A) To properly recognize regions upstream of the gene's transcription start site it requires several general transcription factors that are selective for these regions known as promoters and positions RNAP to accurately begin transcription. (B) These GTF's and other accessory proteins called SRBs are necessary for accurate transcription and together with the RNAP II core enzyme form the RNAP holoenzyme. | ||
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RNA Polymerase was first discovered and isolated by Jerard Hurwitz in 1960. Prior to this, there was research in the synthesis of RNA. One enzyme known as polynucleotide phosphorylase was first isolated. It was initially thought to synthesize RNA but it was later discovered that it was DNA independent and later it was found to degrade RNA. This spurred Hurwitz to search for RNAP using E.coli extracts and in 1960 he showed reproducible RNA synthesis using his extracts and DNA. He published his findings along with three other labs who had also independently worked with RNAP. After this discovery, Hurwitz, along with John J. Furth, purified the enzyme from the E.coli extracts. The purified enzyme catalyzed RNA in the presence of rNTPs, DNA, and magnesium or manganese ions. | RNA Polymerase was first discovered and isolated by Jerard Hurwitz in 1960. Prior to this, there was research in the synthesis of RNA. One enzyme known as polynucleotide phosphorylase was first isolated. It was initially thought to synthesize RNA but it was later discovered that it was DNA independent and later it was found to degrade RNA. This spurred Hurwitz to search for RNAP using E.coli extracts and in 1960 he showed reproducible RNA synthesis using his extracts and DNA. He published his findings along with three other labs who had also independently worked with RNAP. After this discovery, Hurwitz, along with John J. Furth, purified the enzyme from the E.coli extracts. The purified enzyme catalyzed RNA in the presence of rNTPs, DNA, and magnesium or manganese ions. | ||
Initially it was unknown if eukaryotes expressed one type of RNAP like eukaryotes or if there were multiple forms. . In 1969 R. G. Roeder and and W. J. Rutter isolated three distinct species in sea urchin embryos by chromatography. They also showed that they required different environments for optimal activity and the forms are localized to different areas of the nucleus. RNAP I was found in the nucleous and RNAP II and III in the the nucleoplasm. Later experiments also showed that the different species if RNAP responded differently to to the inhibitor alpha-amanitin with RNAP being unresponsive to it, RNAP II inhibited by it, and RNAP II somewhere in between. Using this they could use varying concentrations of alpha-amanitin to see what types of RNA each RNAP was responsible for. | Initially it was unknown if eukaryotes expressed one type of RNAP like eukaryotes or if there were multiple forms. . In 1969 R. G. Roeder and and W. J. Rutter isolated three distinct species in sea urchin embryos by chromatography. They also showed that they required different environments for optimal activity and the forms are localized to different areas of the nucleus. RNAP I was found in the nucleous and RNAP II and III in the the nucleoplasm. Later experiments also showed that the different species if RNAP responded differently to to the inhibitor alpha-amanitin with RNAP being unresponsive to it, RNAP II inhibited by it, and RNAP II somewhere in between. Using this they could use varying concentrations of alpha-amanitin to see what types of RNA each RNAP was responsible for. (E) | ||
== Structural Components == | == Structural Components == | ||
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(E)Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms | (E)Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms | ||
https://www.nature.com/milestones/geneexpression/milestones/articles/milegene07.html | (e)https://www.nature.com/milestones/geneexpression/milestones/articles/milegene07.html | ||
(F)The general transcription factors of RNA | (F)The general transcription factors of RNA | ||
polymerase II | polymerase II | ||
(H)Interactions between the Human RNA Polymerase II Subunits* | |||
Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988 | Bushnell, D. A.; Westover, K. D.; Davis, R. E.; Kornberg, R. D. Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms. Science. 2004, 303, 983-988 | ||
