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Eukaryotic ribosome assembly is a complex multi-step process

Posted by star on 2019-03-06 19:04:48
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    Let us now consider the pathway used to form the ribosome subunits. More than 80 ribosomal proteins are synthesized in the cytoplasm and then imported into the nucleolus. Investigators initially thought that the eukaryotic ribosomes might self-assemble with the assistance of new, if any, nonribosomal proteins. The reason for this expectation was that in Vitro studies showed bacterial ribosomal subunits could assemble spontaneously, without any demonstrable need for cofactors or folding chaperones. However, it soon became evident that eukaryotic ribosome assembly is a complex process that does require assistance from nonribosomal proteins. Although much of our current knowledge of eukaryotic ribosomal assembly comes from studies in yeast, ribosomal assembly in other eukaryotes appears to proceed in a similar fashion.
    Pioneering studies performed independently by the laboratories of Jonathan Warner and Rudi J. planta in the 1970s identified the earliest pre-ribosomal assembly, the 90S particle, so-named because of its sedimentation in a sucrose gradient. This particle, which contains the 35S pre-rRNA as well as many ribosomal proteins, has a relatively high ratio of protein to RNA compared to mature ribosomes. The high protein composition suggested that the 90S particle have additional nonribosomal proteins that are lost when the 90S particle move from the nucleolus to the cytoplasm. These early studies also showed that the 90S particles,the precursors to the mature 60S and 40S subunits,respectively. The technology available in the 1970s and for the next two decades was unable to provide much information about the composition of 90S particles and the nonribosomal proteins associated with them. The chief difficulty was in isolating the intact 90S particle and other pre-ribosome assemblies free from contaminants.
    A new technique known as tandem affinity purification(TAP),which was devised by Bertrand ......


    The precise sequence of events leading to the initiation of rRNA synthesis is not certain. Until recently, the model was that UBF binds to the ribosomal DNA (rDNA) first and then helps to recruit SL1/TIFIB. However, Joost C. B. M. Zomerdijk and coworkers have now demonstrated that UBF itself does not bind stably to rDNA but instead rapidly associates and dissociates. They further demonstrate that SL1/TIFIB to stabilize the binding of UBF to the rDNA promoter. Based on these findings, they question the idea that UBF activates transcription through recruitment of SL1/TIFIB at the rDNA promoter and instead propose alternative model in which SL1/TIFIB directs the formation of the pre-initiation complex by binding to the core promoter, helps to stabilize the binding of UBF and then acts together with UBF to recruit RNA polymerase I .
    Once the pre-initiation complex has assembled the RNA polymerase I machinery is ready to initiate transcription. DNA flanking the transcription initiation site melts to create a small bubble that allows nucleotides to align with the template strand and the first phosphodiester bond is formed. The transcription bubble grows longer as RNA polymerase I moves along the DNA so that the transcription bubble eventually becomes 12 to 23 bp long. RNA polymerase I moves down the template strand, leaving UBF and SL1 behind. At least one additional factor, elongation factor SIL, associates with the transcription elongation complex. Thus, elongation factor SⅡ participates in transcription elongation by both RNA polymerases I and Ⅱ. The elongation rate for human RNA polymerase I has been estimated to be about 95 nucleotides/s. Transcription elongation continues until the RNA polymerase I machinery reaches the transcription terminator. Then transcription is terminated and the transcript and RNA polymerase I are released. The released polymerase is free to reinitiate transcription from a previously activated and......

Ribosomal RNA transcription and processing takes place in the nucleolus

Posted by star on 2019-01-24 19:12:40
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    Active rRNA transcription units and the RNA polymerase I transcription machinery are located within a well-defined transcription and processing "factory" within the nucleus called the nucleolus. Although sometimes referred to as an organelle, the nucleolus is not a true organelle because it is not surrounded by a membrane. When viewed by electron microscopy, the nucleolus has three distinct and conserved structural components. The first of these, the fibrillar center (FC), is a pale region that is enriched with RNA polymerase I and various transcription factors. A nucleolus may have many fibrillar centers. The second structural component, the dense fibrillar component (DFC), is a very dense fibrillar region that partially or completely surrounds the FC. The third structural component, the granular compartment (GC) occupies the rest of the nucleolus. This architecture has been proposed to reflect the vectorial maturation of the pre-ribosomes. According to one hypothesis, RNA synthesis takes piace at the interface between the FC and the DFC, with nascent transcripts extending into the body of the DFC and nascent pre-ribosomes moving from the DFC to the GC as the pre-rRNA is processed, modified, and assembled into a ribosome. The nucleolus is a dynamic structure that is dismantled during mitosis and reassembled at interphase. Its appearance provides clues to certain pathological conditions. For instance, cancer cells often have abnormally large nucleoli. With this background information in mind, we are now ready to examine the enzymes and protein factors involved in pre-RNA formation.




    The eukaryotic cytoplasmic ribosome, which has a molecular mass of about 4 x 106 Da and a sedimentation coefficient of 80S, consists of one small and one large subunit. Small or 40S subunits, which are fairy constant in size (approximately 1.5 X 106 Da) in ribosomes from all eukaryotes, contain an 18S rRNA (approximately 1900 nucleotides) and about 33 different polypeptides. Large or 60S subunits vary in size from one species to another. For instance, large subunits in plants and mammals have molecular masses of 2.5 x 106 Da and 3.0 X 106 Da, respectively. Part of this size variation is due to variations in the size of the largest of the three rRNA molecules in the large subunit. This rRNA is about 5000 nucleotides long (sedimentation coefficient 28S) in mammals but only 3400 nucleotides long (sedimentation coefficient 25S) in yeast. The two other rRNA components in the large subunit are the 5.8S rRNA (approximately 160 nucieotides) and the 5S rRNA (approximately 120 nucleotides). Large subunits from mammals also have about 50 polypeptide subunits, whereas those from lower eukaryotes have somewhat fewer polypeptides. The 5.8S, 18S, and 25S/28S rRNAs are synthesized by RNA polymerase I, whereas the 5s rRNA is synthesized by RNA polymerase I, whereas the 5S rRNA is synthesized by RNA polymerase III.




    Transcriptional processing and RNA editing have important consequences for the eukaryotic proteome (the complete set of proteins expressed during an organism's lifetime). The best current estimate is that the human genome contains approximately 35, 000 transcription units that code for proteins. Alternative splicing, which affects at least 42% of the pre-mRNAs, probably results in the production of a few hundred thousand different kinds of proteins in the human proteome. RNA editing, alternative transcription initiation sites and alternative transcription termination sites also contribute to protein diversity. Furthermore, many proteins are modified after they are formed to produce additional variants. The most common types of posttranslational modifications are cleavage, phosphorylation, acetylation, glycosylation, and methylation. Thus, knowing a transcription unit's DNA sequence is a starting point for understanding how information is transferred from DNA to protein but it is not sufficient by itself to tell us the exact nature of the proteins that are present in a given cell at some specific time. As we see in the final section of this chapter, the situation is even more complex because even synthesis of mRNA does not guarantee that it will be translated.



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