Related books on 'ribosome'
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publisher: Springer, published: 1991-08-05 ASIN: 3540517790 EAN: 9783540517795 For those working and interested in the field of chloroplast ribosomes, an ideal overview is provided by this text. Topics covered include: Plastid rRNAs and tRNAs; Structure, Organization and Expression of Their Genes; Plastid Ribosomal Proteins and Their Genes in Higher Plants; Plastid Ribosomes and Factors of Algae and of Cyanelles; Functional Aspects; Physiological Aspects. Stressed is the fact that biosynthesis and function of the translational apparatus relies upon two separate genetic systems and thus produce particular regulatory problems with fundamental significance. The evolutionary kinship of chloroplast and prokaryotic ribosomes is described as are some differences between them. |
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publisher: Springer, published: 1998-11-13 ASIN: 3540643656 EAN: 9783540643654 sales rank: 9323028 The mechanism by which ribosomal RNA is synthesized has been a topic of intensive research for nearly 30 years. In 1981 the first in vitro transcription system for ribosomal RNA from a eukaryote - mouse ascites cells - was reported, followed rapidly by similar systems in a variety of other eukaryotes, all revealed by a relatively small number of research groups. This monograph is the first to bring together the results and opinions of all these groups. Though it unavoidably emphasizes the common features of ribosomal RNA transcription between species, the species specificity of the process and nucleolar dominance and its possible mechanism(s) are also discussed. |
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publisher: Humana Press, published: 2010-11-19 ASIN: 1617375551 EAN: 9781617375552 sales rank: 3713549 Due to the vital biological importance of RNA and proteins functioning together within a cell, a protocol volume describing experimental procedures to study their interactions should find a home in many laboratories. RNA-Protein Interaction Protocols, Second Edition updates, complements, and expands upon the popular first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. The expert contributors explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biology™ series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, RNA-Protein Interaction Protocols, Second Edition is an ideal guide for researchers continuing the study of this all-important biological partnership. |
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publisher: Springer, published: 2010-06-16 ASIN: 3642121756 EAN: 9783642121753 sales rank: 5322153 Many plants produce enzymes collectively known as ribosome-inactivating proteins (RIPs). RIPs catalyze the removal of an adenine residue from a conserved loop in the large ribosomal RNA. The adenine residue removed by this depurination is crucial for the binding of elongation factors. Ribosomes modified in this way are no longer able to carry out protein synthesis. Most RIPs exist as single polypeptides (Type 1 RIPs) which are largely non-toxic to mammalian cells because they are unable to enter them and thus cannot reach their ribosomal substrate. In some instances, however, the RIP forms part of a heterodimer where its partner polypeptide is a lectin (Type 2 RIPs). These heterodimeric RIPs are able to bind to and enter mammalian cells. Their ability to reach and modify ribosomes in target cells means these proteins are some of the most potently cytotoxic poisons found in nature, and are widely assumed to play a protective role as part of the host plant’s defenses. RIPs are able to further damage target cells by inducing apoptosis. In addition, certain plants produce lectins lacking an RIP component but which are also cytotoxic. This book focuses on the structure/function and some potential applications of these toxic plant proteins. |
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by: Joseph Brady IV Moore publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-09 ASIN: 1243791101 EAN: 9781243791108 sales rank: 3799028 The inherited bone marrow failure syndromes (IBMFS) encompass a heterogeneous collection of rare disorders characterized by hematological abnormalities, generalized growth delays, and an increased incidence of malignant transformation. These disorders include: Diamond-Blackfan anemia (DBA), Shwachman-Diamond syndrome (SDS), cartilage-hair hypoplasia (CHH), and dyskeratosis congenita (DC). Despite sharing overarching similarities, each of these disorders manifests distinct clinical phenotypes. Similar to their clinical features, the molecular underpinnings of the IBMFS have characteristics that are both shared and distinctive. Aberrations in ribosome synthesis have been associated with each of the IBMFS providing a common molecular target for pathogenic mutations in disease related genes. In some cases, the ribosome appears to be the major target of pathogenic lesions, whereas in others, effects on ribosome synthesis are secondary and appear to have a modifying influence on disease presentation. For example, the primary target of pathogenic lesions in dyskeratosis congenita is telomerase which distinguishes it from other IBMFS. The X-linked form of dyskeratosis congenita, however, affects both telomerase function and ribosome synthesis and is considerably more severe than the somatic forms of the disease that only affect telomerase. Thus, differences in primary targets of pathogenic lesions can account for the distinct clinical presentations of certain IBMFS. In other cases, where ribosome synthesis appears to be the major target of disease causing mutations, the basis for diverse clinical manifestations remains unknown. The body of work presented in this dissertation is focused on Shwachman-Diamond syndrome and Diamond-Blackfan anemia, two IBMFS where defects in ribosome synthesis appear to underlie disease pathophysiology. The approach was to use yeast models of both diseases to explore mechanisms by which ribosome synthesis was affected using the 60S ribosomal subunit as a common molecular target. My studies revealed that 60S subunit biogenesis was affected by distinct mechanisms in the two disease models and that these differences may provide the molecular underpinnings for the distinct clinical presentations observed in DBA and SDS patients. Further studies on the mechanism by which 60S subunit biogenesis was affected in the SDS model have clear implications for the treatment of this disorder. |
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by: M. H. Sarma publisher: Adenine Pr, published: 1988-03 ASIN: 0940030217 EAN: 9780940030213 |
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by: Chiaolong Hsiao publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-03 ASIN: 1243589507 EAN: 9781243589507 This thesis presents my work on deciphering, exploring, and discovering the treasure troves of RNA structural bioinformatics, mainly in the areas of multi-resolution analysis of RNA structure. RNA is amazing. We found that without changing the backbone connectivity, RNA can maintain structural conservation in 3D via topology switches, at a single residue level. I developed a method of representing RNA structure in multiresolution, called the PBR approach (P stands for Phosphate; B stands for Base; R stands for Ribose). In this method, structural data is viewed through a series of resolutions from finest to coarsest. At a single nucleotide resolution (fine resolution), RNA is abstruse and elaborate with structural insertions/deletions, strand clips, and 3,2-switches. The compilation of structural deviations of RNA, called DevLS (Deviations of Local Structure), provides a new descriptive language of RNA structure, allowing one to systematize and investigate RNA structure. At PBR resolution (coarse resolution), fundamental RNA architecture, e.g. A-helix, tetraloop, Kink-turns, E-loop motifs etc., becomes readily observable. Using PBR analysis, a total of 103 tetraloops within the crystal structures of the 23s rRNA of H. marismortui (PDB entry: 1JJ2) and the 70s rRNA of T. thermophilus (PDB entry: 2J00 and 2J01) are found and classified. Combining them, I constructed a 'tetraloop family tree', using a tree formalism, to unify and re-define the tetraloop motif and to represent relationships between tetraloops, as grouped by DevLS. To date, structural alignment of very large RNAs remains challenge due to the large size, intricate backbone choreography, and tertiary interactions. To overcome these obstacles, I developed a concept of structural anchors along with a 'Divide and Conquer' strategy for performing superimposition of 23s rRNAs. Here I use tetraloops as structural anchors. The successful alignment and superimpositions of the 23s rRNAs of T. thermophilus and H. marismortui gives an overall RMSD of atomic positions of 1.2 A. This superimposition utilizes 73% of RNA backbone atoms (around 2129 residues). This accurate superimposition allows me to identify regions of structural conservation and diversity, to determine relationships between structural and sequence variation, and to investigate structural relationships between RNA to RNA, RNA to ions, ions to ions, at atomic resolution. By using principles of inorganic chemistry along with structural alignment technique as described above, a recurrent magnesium-binding motif in large RNAs (the 23S rRNAs from H. marismortui and T. thermophilus , the P4-P6 domain of the tetrahymena Group I intron ribozyme, and a Group II intron ribozyme) is revealed. These magnesium-binding motifs play a critical role in the framework of the Peptidyl Transferase Center of the ribosome by their locations, topologies, and coordination geometries. Features of magnesium-binding motif include (i) bridging phosphate chelation of two magnesium ions in the form of Mg2+(i)-(O1P-P-O2P)-Mg 2+(j), (ii) 10-membered chelation ringsutilizing phosphate groups of adjacent residues as Mg2+ ligands, (iii) crystalline-like Mg2+-Mg2+ proximities, (iv) direct Mg2+-phosphate interactions and Mg2+ dehydration, (v) undulated RNA surfaces with unpaired and unstacked bases, and (vi) and usually, close proximity to site of catalysis. |
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by: Marie-jo Halaby publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-04 ASIN: 1243607009 EAN: 9781243607003 The p53 protein is a tumor suppressor that plays a key role in the regulation of cell cycle arrest, apoptosis, and DNA repair. Under normal conditions, p53 levels are kept low in the cell. However, following a stressful event, such as DNA damage, p53 levels will increase dramatically and it will become activated. While it is known that increased p53 translation is necessary for its accumulation following DNA damage, the mechanisms underlying p53 translation are still poorly understood. In our study, we sought to understand the mechanisms behind increased p53 translation following genotoxic stress. Cap-independent or internal ribosome entry site (IRES)-mediated translation is an important alternative mechanism of translation initiation for the synthesis of proteins needed under stressful conditions. Using a bicistronic reporter vector, we showed that the p53 5'-UTR sequence exhibits IRES activity in both cellular and in vitro systems. We also showed that p53 IRES activity increased following treatment with the DNA damaging agent etoposide, suggesting that IRES-mediated translation is an important mechanism for p53 accumulation following DNA damage. Translation initiation at IRESs is often regulated by proteins known as IRES transacting factors (ITAFs). We have identified two proteins, TCP80 and RHA, that can act as positive p53 ITAFs by binding to the p53 IRES and increasing its activity. Overexpression of TCP80 and RHA led to increased expression and synthesis of p53 in p53-null cells transfected with a p53 expression vector containing the p53 5'-UTR. We also discovered two breast cancer cell lines, ZR75-1 and MDA-MB-175 that harbored wild-type p53, but had defective p53 induction and p53 IRES activity following DNA damage. We found that expression of TCP80 and RHA is low in ZR75-1 and MDA-MB-175 cells and that co-expression of both proteins was required to induce p53 IRES in these two cell lines, indicating that these two proteins cooperate to stimulate p53 IRES activity. Our results suggest an important role for TCP80 and RHA in the regulation of IRES-mediated p53 translation following genotoxic stress. Our findings also suggest that poor expression of TCP80 and RHA may be involved in the development of cancer. |
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by: Douglas R Tanner publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-07 ASIN: 124365287X EAN: 9781243652874 In eubacteria, ribosome stalling on broken messenger RNA transcripts can lead to cell death. The trans-translation quality control mechanism rescues many of these stalled ribosomes. In this process, tmRNA enters stalled ribosomes by mimicking a transfer RNA, accepting the stalled nascent peptide. The ribosome then releases the broken mRNA and resumes translation on a coding region within tmRNA itself. Translation of tmRNA marks the nascent peptide for destruction by the addition of a short proteolysis tag and the ribosome is released at a stop codon within the tmRNA open reading frame. An intriguing aspect of trans-translation is that the ribosome synthesizes one protein from two RNA templates. How is the proper site chosen on tmRNA to resume translation? Do the conserved pseudoknot structures help set the reading frame? Using a genetic selection to assay libraries of tmRNA mutants, we found that stable hairpin structures can functionally replace pseudoknot 1. We conclude that the role of pseudoknot 1 in tmRNA function is purely structural. Our results demonstrate that the inactivity of an RNA mutant designed to destroy a given structure should not be interpreted as proof that the structure is necessary for RNA function. Such mutations may only destabilize a global fold that could be formed equally well by an entirely different, stable structure. Broken mRNAs are not the only cause of ribosome stalling; stalling can also result from nascent peptide interactions with the ribosomal exit tunnel that inhibit peptidyl-transferase activity. SecM, TnaC, and ErmCL all stall ribosomes to regulate the expression of downstream genes. What other peptide sequences can cause ribosome stalling? We modified our tmRNA-based selection to screen libraries of random peptides and identified a number of novel stalling peptides, including the sequence FxxYxIWPP. This sequence interacts with the exit tunnel differently than SecM and TnaC as seen in studies using mutant ribosomes. Like SecM, stalling occurs on this sequence with the next aminoacyl tRNA trapped in the A site but unable to react with the nascent peptide. These results show that a variety of peptides can interact in the exit tunnel and peptidyl-transferase center to regulate ribosome activity. |
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by: Alison E Meyer publisher: ProQuest, UMI Dissertation Publishing, published: 2011-09-07 ASIN: 1243672730 EAN: 9781243672735 Molecular chaperones are a diverse group of proteins that are well known for interacting with newly synthesized polypeptides to aid in their proper folding. In Saccharomyces cerevisiae, the ribosome-associated J-protein, Zuo1, functions in concert with the Hsp70 Ssb in the protection of nascent chains as they exit the ribosome. However, specialized chaperones exist that function in a wide variety of additional roles, including modification of protein:protein interactions. Like Zuo1, here I show that the J-protein Jjj1 is also ribosome-associated and can functionally replace Zuo1. However, in contrast to Zuol, Jjj1 associates primarily with free 60S ribosomal subunits and functions with the Hsp70 Ssa. Furthermore, deletion of JJJ1 (but not of ZUO1) results in accumulation of aberrant ribosome formations called half-mers, which are accompanied by a decrease in total 60S subunits. Deletion of either JJJ1 or the known 60S-biogensis factor, REI1, results in cytosolic accumulation of the normally nuclear pre-60S maturation factor Arx1. Together, these data implicate Jjj1 in 60S ribosomal subunit maturation, specifically in the removal or recycling of Arx1 to the nucleus. As both Jjj1 and Rei1 are involved in the removal or recycling of Arx1, I sought to determine if Jjj1 and Rei1 interact. Purified Jjj1 and Rei1 bound to one another in the absence of additional factors in an in vitro assay. Furthermore, the domains responsible for interaction of Jjj1 with Rei1 include two zinc fingers as well as a region of highly charged amino acids located at the C-terminus of Jjj1. Disruption of this interaction by deletion of the charged region results in accumulation of half-mer ribosomes and concomitant accumulation of Arx1 in the cytosol, however the mutant Jjj1 protein remains ribosome-bound. Together this suggests that the interaction between Jjj1 and Rei1 is important for 60S subunit biogenesis. In addition, I present further evidence that Jjj1, Rei1, and Ssa cooperate in the physical removal of Arx1 from the pre-60S subunits, facilitating its cytosolic maturation. |