- RNA Polymerase Types and Roles in Eukaryotes
Recent X-ray analysis of RNA polymerase has revealed important structural details that help explain the precise mechanism of transcription. Double-helical DNA enters a long cleft in the surface of the enzyme, and is held in place by a large flexible portion of the enzyme termed the "clamp. " Within the cleft, the DNA is separated and RNA is paired to it. A magnesium ion, sitting at the critical point where RNA nucleotides are added to the primary transcript, is thought to help catalyze this reaction. An internal barrier forces a bend in the growing DNA-RNA duplex, exposing the RNA end for addition of the incoming nucleotide. A short protein extension, termed the "rudder, " helps to separate the RNA from the DNA, and the two exit the polymerase along separate paths. The average maximum rate of elongation in bacteria is 5 to 10 nucleotides per second. However, during transcription, the polymerase enzyme may pause for seconds to minutes. These pauses are thought to be part of a regulatory mechanism.
RNA Polymerase Types and Roles in Eukaryotes
Assembly of RNA polymerase II is initiated by the formation of the αα dimer which interacts with the β and forms a bound complex intermediate. The active cleft in the RNA polymerase II is composed of β subunits which are formed in the final step of assembly, so the polymerase will not be catalytically active until it is complete. RNA polymerase II in both bacteria and eukaryotic cells has both exhibited formation in equivalent manner. Assembly in vitro experiments have also been conducted to determine the origins of RNA polymerase II. Using three mutant large subunits, their assembly was followed with the use of pulse chase experiments. Scientists found that Rpb3 and Rpb3 were the first to interact, and the bound complex then interacts with Rpb1. However, because larger mutated subunits were used, final assembly could not be complete without the use of Rpb6, Rpb10, and Rpb12, which are not normally part of final assembly in normal sized RNA polymerase II. If any RNA subunits are lost during its assembly, there will be an excess of Rpb1 present in the cytoplasm, meaning that the polymerase needs to be fully assembled before it is allowed to enter the nucleus and take place in transcriptase.
Gene Silencing: Gene expression regulation at Particular Gene What are Gene Families and How they Evolved? Every molecule of RNA pol holoenzyme contains exactly one sigma factor subunit, which is the model bacterium Escherichia coli is one of those listed below. The number of sigma factors varies between bacterial species. E. coli has seven sigma factors. Sigma factors are distinguished by their characteristic molecular weights. For example, σ70 refers to the sigma factor with a molecular weight of 70 kDa. Specialized Sigma Factors: Sigma factors in E. coli: σ70(RpoD) (or) σA: The " housekeeping " sigma factor or also called as primary sigma factor, transcribes most genes in growing cells. Every cell has a "housekeeping" sigma factor that keeps essential genes and pathways operating. In the case of E. coli and other gram-negative rod-shaped bacteria, the "housekeeping" sigma factor is σ70. Genes recognized by σ70 all contain similar promoter consensus sequences consisting of two parts.
Transcription Transcription begins when RNA polymerase binds to the DNA double helix. This occurs at a site just "upstream" of the gene to be transcribed, called the promoter site. In eukaryotes, RNA polymerase is directed to the promoter site by transcription factors, proteins that bind to the DNA and provide a docking site for attachment of the polymerase enzyme. Once RNA polymerase binds to the DNA at the promoter, transcription can begin. During transcription, the polymerase unwinds a portion of the double-stranded DNA, exposing the DNA template strand that will be copied into RNA. Individual RNA nucleotides enter the enzyme complex, and are paired with the DNA. C pairs with G, T (on DNA) pairs with A, and A (on DNA) pairs with U. Nine DNA-RNA nucleotide pairs exist within the polymerase molecule at any one time. After each new RNA nucleotide is paired, it is linked to the preceding RNA nucleotide, forming a growing strand of polymerized RNA called the primary transcript. This stage of transcription is called elongation.
The result can be likened to an RNA-DNA zipper. The newly formed RNA strand is then "unzipped" from the DNA strand, and it exits the polymerase. The DNA strands rejoin, and the polymerase continues moves along the length of the DNA strand, repeating this process. Messenger RNA is a copy of a DNA sequence, which is located in the genetic material in the nucleus of a cell. The process is sometimes disrupted. Viruses that alter gene expression often do so by shutting off the transcription process of RNA polymerase II. The influenza virus, for instance, has been found to inhibit and destroy this particular polymerase in some cases. One of several types of macromolecules, RNA polymerase II is actually a large complex made of 10 different protein sub-units. It transcribes messenger RNAs and several small nuclear RNAs. This is just one of several types of polymerases. The highly contagious influenza virus may inhibit and destroy RNA polymerase II. RNA polymerase II differs from RNA polymerase III, whose function is mostly to regulate cell growth.
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