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RNA Polymerase Transcription



Image of RNA polymerase from the journal Science.


RNA Polymerase transcribes genetic information into a message that can be read by the ribosome to produce protein. The research group of Professor Roger Kornberg of Stanford University has studied the structure of this 12-subunit and half-megadalton size macromolecular machine using diffraction data collected by the Stanford Synchrotron Radiation Lightsource (SSRL). A key step in gene 1) ___ is the “transcription” of the DNA sequences comprising the genes into messenger RNAs. Transcription is the first step and a key control point in gene expression. Transcriptional regulation underlies all aspects of cellular metabolism including oncogenesis (cancer) and morphogenesis (development). RNA polymerase II (Pol II) is a large (550 kDa) complex of 12 subunits that is at the heart of the transcription mechanism. Gene expression, and therefore RNA pol II, is regulated by a number of proteins, in particular initiation and transcription factors.


The interpretation of the structural and biochemical experiments have resulted in a number of breakthrough publications. Jean Marx, as reported in of Science Magazine (Science Apr 20 2001: 411-414), describes this remarkable structure in the following way:


“If any enzyme does the cell’s heavy lifting, it’s RNA polymerase II. Its job: getting the synthesis of all the proteins in higher cells under way by copying their genes into RNAs, and doing it at just the right time and in just the right amounts. As such, pol II, as the enzyme is called, is the heart of the machinery that controls everything that 2) ___ do from differentiating into all the tissues of a developing embryo to responding to everyday stresses. Now, cell biologists can get their best look yet at just how the pol II enzyme of yeast and, by implication, of other higher organisms performs its critical role.”




Simplified diagram of mRNA synthesis and processing. Enzymes not shown.


Transcription is the first step of gene expression, in which a particular segment of 3) ___ is copied into RNA by the enzyme RNA polymerase. Both RNA and DNA are nucleic 4) ___, which use base pairs of nucleotides as a complementary language. The two can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene transcribed, encodes a protein, messenger RNA (mRNA) will be transcribed; the mRNA will in turn serve as a template for the protein’s synthesis through translation. Alternatively, the transcribed gene may encode for either non-coding RNA (such as microRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), or other ribozymes. Overall, RNA helps synthesize, regulate, and process 5) ___; it therefore plays a fundamental role in performing functions within a cell. In eukaryotes, RNA polymerase, and therefore the initiation of transcription, requires the presence of a core promoter sequence in the DNA. Promoters are regions of DNA that promote transcription and, in eukaryotes, are found at -30, -75, and -90 base pairs upstream from the transcription start site (abbreviated to TSS). Core promoters are sequences within the promoter that are essential for transcription initiation. RNA polymerase is able to bind to core promoters in the presence of various specific transcription factors. One strand of the DNA, the template strand (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template 6) ___ and uses base pairing complementary with the DNA template to create an RNA copy.




In bacteria, transcription begins with the binding of RNA polymerase to the promoter in DNA. RNA polymerase is a core enzyme consisting of five subunits. Transcription inhibitors can be used as 7) ___ against, for example, pathogenic bacteria (antibacterials) and fungi (antifungals). An example of such an antibacterial is rifampicin, which inhibits prokaryotic DNA transcription into mRNA by inhibiting DNA-dependent RNA polymerase by binding its beta-subunit.


Prokaryotes (bacteria) have no 8) ___ and eukaryotic transcription is more complex than prokaryotic transcription. For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (in which translation occurs) by the nuclear membrane. This allows for the temporal regulation of gene expression through the sequestration of the RNA in the nucleus, and allows for selective transport of mature RNAs to the cytoplasm. Bacteria on the other hand do not have a distinct nucleus that separates DNA from ribosome and mRNA is translated into protein as soon as it is transcribed. The coupling between the two processes provides an important mechanism for prokaryotic gene regulation.


Transcription is the process of copying genetic information stored in a DNA strand into a transportable complementary strand of RNA. Eukaryotic transcription takes place in the nucleus of the cell and proceeds in three sequential stages: initiation, elongation, and termination. The transcriptional machinery that catalyzes this complex reaction has at its core three multi-subunit RNA polymerases. RNA polymerase I is responsible for transcribing RNA that codes for genes that become structural components of the ribosome, a protein responsible for the translation of RNA into proteins.


Protein coding genes are transcribed into messenger RNAs (mRNAs) that carry the information from DNA to the site of protein synthesis. Although mRNAs possess great diversity, they are not the most abundant RNA species made in the cell. The so-called non-coding RNAs account for the large majority of the transcriptional output of a cell. These non-coding 9) ___ perform a variety of important cellular functions. Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes (including humans) comes in three variations, each encoding a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.


A molecule that allows the genetic material to be realized as a protein was first hypothesized by Fran?ois Jacob and Jacques Monod. Arthur Kornberg and Severo Ochoa won a Nobel Prize in Physiology or Medicine in 1959 for developing a process for synthesizing RNA in vitro with polynucleotide phosphorylase, which was useful for cracking the genetic 10) ___. RNA synthesis by RNA polymerase was established in vitro at several laboratories by 1965; however, the RNA synthesized by these enzymes had properties that suggested the existence of an additional factor needed to terminate transcription correctly. In 1972, Walter Fiers became the first person to actually prove the existence of the terminating enzyme. Roger D. Kornberg won the 2006 Nobel Prize in Chemistry “for his studies of the molecular basis of eukaryotic transcription”.


Cell Overview (http://vcell.ndsu.nodak.edu/animations/flythrough/movie-flash.htm)


Animation of gene transcription (http://highered.mheducation.com/olc/dl/120069/bio06.swf)


Transcription (http://vcell.ndsu.nodak.edu/animations/transcription/movie-flash.htm)



1) expression; 2) cells; 3) DNA; 4) acids; 5) protein; 6) strand; 7) antibiotics; 8) nucleus; 9) RNAs; 10) code



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