Bibliografías temáticas / Ribosomal RNAs

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Literatura académica sobre el tema "Ribosomal RNAs"

Autor: Grafiati

Publicado: 25 de mayo de 2024

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Artículos de revistas sobre el tema "Ribosomal RNAs"

Lejars, Maxence, Asaki Kobayashi y Eliane Hajnsdorf. "RNase III, Ribosome Biogenesis and Beyond". Microorganisms 9, n.º 12 (17 de diciembre de 2021): 2608. http://dx.doi.org/10.3390/microorganisms9122608.

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The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III.

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Moritz, M., A. G. Paulovich, Y. F. Tsay y J. L. Woolford. "Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly." Journal of Cell Biology 111, n.º 6 (1 de diciembre de 1990): 2261–74. http://dx.doi.org/10.1083/jcb.111.6.2261.

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Two strains of Saccharomyces cerevisiae were constructed that are conditional for synthesis of the 60S ribosomal subunit protein, L16, or the 40S ribosomal subunit protein, rp59. These strains were used to determine the effects of depriving cells of either of these ribosomal proteins on ribosome assembly and on the synthesis and stability of other ribosomal proteins and ribosomal RNAs. Termination of synthesis of either protein leads to diminished accumulation of the subunit into which it normally assembles. Depletion of L16 or rp59 has no effect on synthesis of most other ribosomal proteins or ribosomal RNAs. However, most ribosomal proteins and ribosomal RNAs that are components of the same subunit as L16 or rp59 are rapidly degraded upon depletion of L16 or rp59, presumably resulting from abortive assembly of the subunit. Depletion of L16 has no effect on the stability of most components of the 40S subunit. Conversely, termination of synthesis of rp59 has no effect on the stability of most 60S subunit components. The implications of these findings for control of ribosome assembly and the order of assembly of ribosomal proteins into the ribosome are discussed.

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Jovanovic, Bogdan, Lisa Schubert, Fabian Poetz y Georg Stoecklin. "Tagging of RPS9 as a tool for ribosome purification and identification of ribosome-associated proteins". Archives of Biological Sciences, n.º 00 (2020): 57. http://dx.doi.org/10.2298/abs20120557j.

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Ribosomes, the catalytic machinery required for protein synthesis, are comprised of 4 ribosomal RNAs and about 80 ribosomal proteins in mammals. Ribosomes further interact with numerous associated factors that regulate their biogenesis and function. As mutations of ribosomal proteins and ribosome associated proteins cause many diseases, it is important to develop tools by which ribosomes can be purified efficiently and with high specificity. Here, we designed a method to purify ribosomes from human cell lines by C-terminally tagging human RPS9, a protein of the small ribosomal subunit. The tag consists of a flag peptide and a streptavidin-binding peptide (SBP) separated by the tobacco etch virus (TEV) protease cleavage site. We demonstrate that RPS9-Flag-TEV-SBP (FTS) is efficiently incorporated into the ribosome without interfering with regular protein synthesis. Using HeLa-GFP-G3BP1 cells stably expressing RPS9-FTS or, as a negative control, mCherry-FTS, we show that complete ribosomes as well as numerous ribosome-associated proteins are efficiently and specifically purified following pull-down of RPS9-FTS using streptavidin beads. This tool will be helpful for the characterization of human ribosome heterogeneity, post-translational modifications of ribosomal proteins, and changes in ribosome-associated factors after exposing human cells to different stimuli and conditions.

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Pollutri, Daniela y Marianna Penzo. "Ribosomal Protein L10: From Function to Dysfunction". Cells 9, n.º 11 (19 de noviembre de 2020): 2503. http://dx.doi.org/10.3390/cells9112503.

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Eukaryotic cytoplasmic ribosomes are highly structured macromolecular complexes made up of four different ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs), which play a central role in the decoding of genetic code for the synthesis of new proteins. Over the past 25 years, studies on yeast and human models have made it possible to identify RPL10 (ribosomal protein L10 gene), which is a constituent of the large subunit of the ribosome, as an important player in the final stages of ribosome biogenesis and in ribosome function. Here, we reviewed the literature to give an overview of the role of RPL10 in physiologic and pathologic processes, including inherited disease and cancer.

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Moraleva, Anastasia A., Alexander S. Deryabin, Yury P. Rubtsov, Maria P. Rubtsova y Olga A. Dontsova. "Eukaryotic Ribosome Biogenesis: The 40S Subunit". Acta Naturae 14, n.º 1 (10 de mayo de 2022): 14–30. http://dx.doi.org/10.32607/actanaturae.11540.

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The formation of eukaryotic ribosomes is a sequential process of ribosomal precursors maturation in the nucleolus, nucleoplasm, and cytoplasm. Hundreds of ribosomal biogenesis factors ensure the accurate processing and formation of the ribosomal RNAs tertiary structure, and they interact with ribosomal proteins. Most of what we know about the ribosome assembly has been derived from yeast cell studies, and the mechanisms of ribosome biogenesis in eukaryotes are considered quite conservative. Although the main stages of ribosome biogenesis are similar across different groups of eukaryotes, this process in humans is much more complicated owing to the larger size of the ribosomes and pre-ribosomes and the emergence of regulatory pathways that affect their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. This review addresses the key aspects of yeast and human ribosome biogenesis, using the 40S subunit as an example. The mechanisms underlying these differences are still not well understood, because, unlike yeast, there are no effective methods for characterizing pre-ribosomal complexes in humans. Understanding the mechanisms of human ribosome assembly would have an incidence on a growing number of genetic diseases (ribosomopathies) caused by mutations in the genes encoding ribosomal proteins and ribosome biogenesis factors. In addition, there is evidence that ribosome assembly is regulated by oncogenic signaling pathways, and that defects in the ribosome biogenesis are linked to the activation of tumor suppressors.

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Shatskikh, Aleksei S., Elena A. Fefelova y Mikhail S. Klenov. "Functions of RNAi Pathways in Ribosomal RNA Regulation". Non-Coding RNA 10, n.º 2 (29 de marzo de 2024): 19. http://dx.doi.org/10.3390/ncrna10020019.

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Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.

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Konikkat, Salini y John L. Woolford,. "Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast". Biochemical Journal 474, n.º 2 (6 de enero de 2017): 195–214. http://dx.doi.org/10.1042/bcj20160516.

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Ribosome biogenesis requires the intertwined processes of folding, modification, and processing of ribosomal RNA, together with binding of ribosomal proteins. In eukaryotic cells, ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is not completed until after nascent particles are exported to the cytoplasm. The efficiency and fidelity of ribosome biogenesis are facilitated by >200 assembly factors and ∼76 different small nucleolar RNAs. The pathway is driven forward by numerous remodeling events to rearrange the ribonucleoprotein architecture of pre-ribosomes. Here, we describe principles of ribosome assembly that have emerged from recent studies of biogenesis of the large ribosomal subunit in the yeast Saccharomyces cerevisiae. We describe tools that have empowered investigations of ribosome biogenesis, and then summarize recent discoveries about each of the consecutive steps of subunit assembly.

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Roychowdhury, Amlan, Clément Joret, Gabrielle Bourgeois, Valérie Heurgué-Hamard, Denis L. J. Lafontaine y Marc Graille. "The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis". Nucleic Acids Research 47, n.º 14 (12 de junio de 2019): 7548–63. http://dx.doi.org/10.1093/nar/gkz529.

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Abstract Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.

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Collins, Jason C., Homa Ghalei, Joanne R. Doherty, Haina Huang, Rebecca N. Culver y Katrin Karbstein. "Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head". Journal of Cell Biology 217, n.º 12 (22 de octubre de 2018): 4141–54. http://dx.doi.org/10.1083/jcb.201804163.

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The correct assembly of ribosomes from ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) is critical, as indicated by the diseases caused by RP haploinsufficiency and loss of RP stoichiometry in cancer cells. Nevertheless, how assembly of each RP is ensured remains poorly understood. We use yeast genetics, biochemistry, and structure probing to show that the assembly factor Ltv1 facilitates the incorporation of Rps3, Rps10, and Asc1/RACK1 into the small ribosomal subunit head. Ribosomes from Ltv1-deficient yeast have substoichiometric amounts of Rps10 and Asc1 and show defects in translational fidelity and ribosome-mediated RNA quality control. These defects provide a growth advantage under some conditions but sensitize the cells to oxidative stress. Intriguingly, relative to glioma cell lines, breast cancer cells have reduced levels of LTV1 and produce ribosomes lacking RPS3, RPS10, and RACK1. These data describe a mechanism to ensure RP assembly and demonstrate how cancer cells circumvent this mechanism to generate diverse ribosome populations that can promote survival under stress.

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Leclerc, Daniel y Léa Brakier-Gingras. "Study of the function of Escherichia coli ribosomal RNA through site-directed mutagenesis". Biochemistry and Cell Biology 68, n.º 1 (1 de enero de 1990): 169–79. http://dx.doi.org/10.1139/o90-023.

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Various approaches have been developed to study how mutations in Escherichia coli ribosomal RNA affect the function of the ribosome. Most of them are in vivo approaches, where mutations are introduced in a specialized plasmid harboring the ribosomal RNA genes. The mutated plasmids are then expressed in an appropriate host, where they can confer resistance to antibiotics whose target is the ribosome. Conditions can be used where the host ribosomal RNA genes or the host ribosomes are selectively inactivated, and the effect of the mutations on ribosome assembly and function can be studied. Another approach, which has been developed mainly with 16S ribosomal RNA, can be used entirely in vitro. In this approach, a plasmid has been constructed which contains the 16S ribosomal RNA gene under control of a T7 promoter. Mutations can be introduced in the 16S ribosomal RNA sequence and the mutated 16S ribosomal RNAs are produced by in vitro transcription. It is then possible to investigate how the mutations affect the assembly of the 16S ribosomal RNA into 30S subunits and the activity of the reconstituted 30S subunits in cell-free protein synthesis assays. Although these approaches are recent, they have already provided a large body of interesting information, relating specific RNA sequences to interactions with ribosomal proteins, to ribosome function, and to its response to antibiotics.Key words: ribosomal RNA, ribosome, site-directed mutagenesis, antibiotic resistance.

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Tesis sobre el tema "Ribosomal RNAs"

Slinger, Betty L. "Insights into the Co-Evolution of Ribosomal Protein S15 with its Regulatory RNAs". Thesis, Boston College, 2016. http://hdl.handle.net/2345/bc-ir:106793.

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Thesis advisor: Michelle M. Meyer
Ribosomes play a vital role in all cellular life translating the genetic code into functional proteins. This pivotal function is derived from its structure. The large and small subunits of the ribosome consist of 3 ribosomal RNA strands and over 50 individual ribosomal proteins that come together in a highly coordinated manner. There are striking differences between eukaryotic and prokaryotic ribosomes and many of the most potent antibacterial drugs target bacterial ribosomes (e.g. tetracycline and kanamycin). Bacteria spend a large amount of energy and nutrients on the production and maintenance of these molecular machines: during exponential growth as much as 40% of dry bacterial mass is ribosomes (Harvey 1970). Because of this, bacteria have evolved an elegant negative feedback mechanism for the regulation of their ribosomal proteins, known as autoregulation. When excess ribosomal protein is produced, unneeded for ribosome assembly, the protein binds a structured portion of its own mRNA transcript to prevent further expression of that operon. Autoregulation facilitates a quick response to changing environmental conditions and ensures economical use of nutrients. My thesis has investigated the autoregulatory function of ribosomal protein S15 in diverse bacterial phyla. In many bacterial species, when there is excess S15 the protein interacts with an RNA structure formed in the 5’-UTR of its own mRNA transcript that enables autoregulation of the S15-encoding operon, rpsO. For many ribosomal proteins (ex. L1, L20, S2) there is striking homology and often mimicry between the recognition motifs within the rRNA and the regulatory mRNA structure. However, this is not the case for S15-three different regulatory RNA structures have been previously described in E. coli, G. stearothermophilus, and T. thermophilus (Portier 1990, Scott 2001, Serganov 2003). These RNAs share little to no structural homology to one another, nor the rRNA, and they are narrowly distributed to their respective bacterial phyla, Gammaproteobacteria, Firmicutes, and Thermales. It is unknown which regulatory RNA structures control the expression of S15 outside of these phyla. Additionally, previous work has shown the S15 homolog from G. stearothermophilus is unable to regulate expression using the mRNA from E. coli. These observations formulate the crux of the question this thesis work endeavors to answer: What drove the evolution of such diverse regulatory RNA structures in these different bacteria? In Chapter II, “Discover and Validate Novel Regulatory Structures for Ribosomal Protein S15in Diverse Bacterial Phyla”, I present evidence for the in silico identification of three novel regulatory RNA structures for S15 and present experimental evidence that one of these novel structures is distinct from those previously described. In Chapter III, “Co-evolution of Ribosomal Protein S15 with Diverse Regulatory RNA Structures”, I present evidence that the amino acid differences in S15 homologs contribute to differences in mRNA binding profiles, and likely lead to the development of the structurally diverse array of the regulatory RNAs we observe in diverse bacterial phyla. In Chapter IV, “Synthetic cis-regulatory RNAs for Ribosomal Protein S15”, I investigate the derivation of novel cis-regulatory RNAs for S15 and find novel structures are readily-derived, yet interact with the rRNA-binding face of S15. Together the work presented in this thesis advances our understanding of the co-evolution between ribosomal protein S15 and its regulatory RNAs in diverse bacterial phyla
Thesis (PhD) — Boston College, 2016
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

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Girnary, Roseanne Waheeda. "Structural and functional studies of the stimulatory RNAs involved in programmed -1 ribosomal frameshifting and translational readthrough". Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612716.

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Huang, Hsiau-Wen. "Investigation of solution structures of yeast and lupin seed 5S ribosomal RNAs by high resolution nuclear magnetic resonance and molecular dynamics simulation /". The Ohio State University, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487684245468516.

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Crandall, Jacob N. "Ribosomal RNA Mutations that Inhibit the Activity of Transfer-Messenger RNA of Stalled Ribosomes". Diss., CLICK HERE for online access, 2010. http://contentdm.lib.byu.edu/ETD/image/etd3535.pdf.

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Roy, Poorna. "Deconstructing the ribosome: specific interactions of a ribosomal RNA fragment with intact and fragmented L23 ribosomal protein". Thesis, Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47579.

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The complexity of translation is a classical dilemma in the evolution of biological systems. Efficient translation requires coordination of complex, highly evolved RNAs and proteins; however, complex, highly evolved RNAs and proteins could not evolve without efficient translation system. At the heart of this complexity is the ribosome, itself a remarkably complex molecular machine. Our work illustrates the ribosome as deconstructed units of modification. Here we have deconstructed a segment of the ribosome to interacting RNA-protein units. L23 interacts in vivo with both Domain III (DIII) and Domain IIIcore (DIIIcore) independently of the fully assembled ribosome. This suggests that DIIIcore represents the functional rRNA unit in DIII-L23 interaction. Furthermore, L23peptide sustains binding function in vitro with both DIII and DIIIcore independently of any stabilizing effects from the globular domain of L23. The ability of L23peptide to form a 1:1 complex with both DIII and DIIIcore suggests that L23peptide is the functional rProtein unit in DIII-L23 interaction. We believe that our results will stimulate interest and discussions in the significance of 3D architecture and units of evolution in the ribosome. The ubiquity of the ribosome in cellular life prognosticates that our results impact and appeal to biologists, chemists, bioinformaticists, as well as the general scientific community.

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Burlacu, Elena. "Probing ribosomal RNA structural rearrangements : a time lapse of ribosome assembly dynamics". Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/17072.

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Ribosome synthesis is a very complex and energy consuming process in which pre-ribosomal RNA (pre-rRNA) processing and folding events, sequential binding of ribosomal proteins and the input of approximately 200 trans-acting ribosome assembly factors need to be tightly coordinated. In the yeast Saccharomyces cerevisiae, ribosome assembly starts in the nucleolus with the formation of a very large 90S-sized complex. This ~2.2MDa pre-ribosomal complex is subsequently processed into the 40S and 60S assembly intermediates (pre-40S and pre-60S), which subsequently mature largely independently. Although we have a fairly complete picture of the protein composition of these pre-ribosomes, still very little is known about the rRNA structural rearrangements that take place during the assembly of the 40S and 60S subunits and the role of the ribosome assembly factors in this process. To address this, the Granneman lab developed a method called ChemModSeq, which made it possible to generate nucleotide resolution maps of RNA flexibility in ribonucleoprotein complexes by combining SHAPE chemical probing, high-throughput sequencing and statistical modelling. By applying ChemModSeq to ribosome assembly intermediates, we were able to obtain nucleotide resolution insights into rRNA structural rearrangements during late (cytoplasmic) stages of 40S assembly and for the early (nucleolar) stages of 60S assembly. The results revealed structurally distinct cytoplasmic pre-40S particles in which rRNA restructuring events coincide with the hierarchical dissociation of assembly factors. These rearrangements are required to trigger stable incorporation of a number of ribosomal proteins and the completion of the head domain. Rps17, one of the ribosomal proteins that fully assembled into pre-40S complexes only at a later assembly stage, was further characterized. Surprisingly, my ChemModSeq analyses of nucleolar pre-60S complexes indicated that most of the rRNA folding steps take place at a very specific stage of maturation. One of the most striking observations was the stabilization of 5.8S pre-rRNA region, which coincided with the dissociation of the assembly factor Rrp5 and stable incorporation of a number of ribosomal proteins.

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Ramesh, Madhumitha. "Analysis of Ribosome Biogenesis from Three Standpoints: Investigating the Roles of Ribosomal RNA, Ribosomal Proteins and Assembly Factors". Research Showcase @ CMU, 2016. http://repository.cmu.edu/dissertations/609.

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Ribosomes are ubiquitous and abundant molecular machines composed of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins). They play a central role in the cell by translating the genetic code in mRNA to form polypeptides. Because of their large size and the complexity of molecular interactions within ribosomes, we do not still fully understand how they are synthesized in the cell. Yet, a thorough knowledge of ribosome biogenesis is crucial to understand cellular homeostasis and various disease states including ribosomopathies and cancer. In addition, ribosomes serve as an interesting paradigm to understand the principles that dictate the formation and function of the many different ribonucleoprotein particles that play vital roles in the cell. In addition to the rRNA and r-protein components, trans-acting assembly factors play indispensable roles in synthesizing functional ribosomes. Fundamentally, ribosome biogenesis is driven by a network of molecular interactions that evolve in time and space, as assembly progresses from the nucleolus to the cytoplasm. We sought to gain a deeper understanding of ribosome biogenesis in Saccharomyces cerevisiae by investigating the molecular interactions that drive ribosome assembly. Recent structural studies have revealed a number of such molecular interactions at high resolution. Based on these, our investigation was carried out from the perspectives of all three players that are involved in constructing ribosomes, with a specific emphasis on eukaryote-specific elements of rRNAs and r-proteins. From the standpoint of rRNA, we performed the first systematic study to investigate the potential functions of nearly all of the eukaryotic rRNA expansion segments in the yeast large ribosomal subunit. We showed that most of them are indispensable and play vital roles in ribosome biogenesis. Based on the steps of ribosome biogenesis in which each of them participates, we showed that there is neighborhood-specific functional clustering of rRNA and r-protein interactions that drive ribosome assembly. Further, we found evidence for possible functional co-evolution of eukaryotic rRNA and eukaryote-specific elements of r-protein. From the standpoint of r-protein, we used rpL5 as a paradigm for constantly evolving molecular interactions as assembly progresses. Apart from recapitulating Diamond-Blackfan anemia missense mutations in yeast, we characterized interactions formed by specific regions of rpL5 and propose that these interactions potentially govern the loading of 5S RNP en bloc to the nascent large ribosomal subunit, to ensure proper rotation of the 5S RNP during biogenesis, and to further recruit proteins necessary for the test drive of subunits in the cytoplasm. From the standpoint of assembly factors, we analyzed a so-called group of ITS2 cluster proteins, Nop15, Cic1 and Rlp7 and identified the extensive protein-protein interactions and analyzed protein-RNA interactions that they make. Using our data, we were able to localize Rlp7 to the ITS2 spacer in the pre-rRNA and to identify potential mechanisms for their function. Having identified a network of molecular interactions, we suggest that these proteins orchestrate proper folding of rRNA through this network, and stabilize and facilitate the early steps of assembly. Further, based on their location in the preribosome, these factors might serve to ensure proper progression of early steps of assembly to enable subsequent processing of the ITS2 spacer in the middle steps, possibly by recruiting the ATPase Has1. Thus, we have investigated early nucleolar and late nuclear steps of ribosome assembly in the light of molecular interactions formed by rRNA, r-protein and assembly factors that participate in eukaryotic ribosome assembly. Lessons that emerged from this study and tools developed in the process provide a starting point for further investigations pertaining to the roles of eukaryote-specific segments of molecules that participate in ribosome biogenesis, and serve as a paradigm for how a dynamic network of molecular interactions can drive the assembly of complex macromolecular structures.

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Weaver, Paul L. "Characterization of a putative RNA helicase, Dbp3p, in ribosomal RNA processing and ribosome biogenesis in Saccharomyces Cerevisiae /". The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu148794750113696.

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G, C. Keshav. "Investigation of the Role of Bacterial Ribosomal RNA Methyltransferase Enzyme RsmC in Ribosome Biogenesis". Kent State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=kent1621868567263046.

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Kshetri, Man B. "N-TERMINAL DOMAIN OF rRNA METHYLTRANSFERASE ENZYME RsmC IS IMPORTANT FOR ITS BINDING TO RNA AND RNA CHAPERON ACTIVITY". Kent State University Honors College / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1621007414429417.

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Más fuentes

Libros sobre el tema "Ribosomal RNAs"

A, Zimmermann Robert y Dahlberg Albert E, eds. Ribosomal RNA: Structure, evolution, processing, and function in protein biosynthesis. Boca Raton: CRC Press, 1996.

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Rodnina, Marina V., Wolfgang Wintermeyer y Rachel Green. Ribosomes: Structure, function, and dynamics. Editado por Ribosomes Meeting (2010 : Orvieto, Italy). Wien: Springer, 2011.

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Transcription of ribosomal RNA genes by eukaryotic RNA polymerase I. Berlin: Springer, 1998.

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1943-, Paule Marvin R., ed. Transcription of ribosomal RNA genes by eukaryotic RNA polymerase I. Berlin: Springer, 1998.

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RNA-RNA interactions: Methods and protocols. New York: Humana Press, 2015.

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Baylis, Howard Andrew. The ribosomal RNA genes of Streptomyces coelicolor A3(2). Norwich: University of East Anglia, 1986.

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Firek, Simon. The promotion of ribosomal RNA transcription in Xenopus laevis. Portsmouth: Portsmouth Polytechnic,School of Biological Sciences, 1989.

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Ribosome display and related technologies: Methods and protocols. New York: Humana Press, 2012.

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Måns, Ehrenberg, ed. Structural aspects of protein synthesis. 2^a ed. New Jersey: World Scientific, 2013.

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Structural aspects of protein synthesis. Singapore: World Scientific, 2005.

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Capítulos de libros sobre el tema "Ribosomal RNAs"

Merkl, Philipp E., Christopher Schächner, Michael Pilsl, Katrin Schwank, Catharina Schmid, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck y Herbert Tschochner. "Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae". En Ribosome Biogenesis, 63–70. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_4.

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AbstractIn archaea and bacteria the major classes of RNAs are synthesized by one DNA-dependent RNA polymerase (RNAP). In contrast, most eukaryotes have three highly specialized RNAPs to transcribe the nuclear genome. RNAP I synthesizes almost exclusively ribosomal (r)RNA, RNAP II synthesizes mRNA as well as many noncoding RNAs involved in RNA processing or RNA silencing pathways and RNAP III synthesizes mainly tRNA and 5S rRNA. This review discusses functional differences of the three nuclear core RNAPs in the yeast S. cerevisiae with a particular focus on RNAP I transcription of nucleolar ribosomal (r)DNA chromatin.

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Kitahara, Kei y Kentaro Miyazaki. "Constructing Mutant Ribosomes Containing Mutant Ribosomal RNAs". En Applied RNA Bioscience, 17–32. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-8372-3_2.

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Sharma, Sunny y Karl-Dieter Entian. "Chemical Modifications of Ribosomal RNA". En Ribosome Biogenesis, 149–66. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_9.

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AbstractCellular RNAs in all three kingdoms of life are modified with diverse chemical modifications. These chemical modifications expand the topological repertoire of RNAs, and fine-tune their functions. Ribosomal RNA in yeast contains more than 100 chemically modified residues in the functionally crucial and evolutionary conserved regions. The chemical modifications in the rRNA are of three types—methylation of the ribose sugars at the C2-positionAbstract (Nm), isomerization of uridines to pseudouridines (Ψ), and base modifications such as (methylation (mN), acetylation (acN), and aminocarboxypropylation (acpN)). The modifications profile of the yeast rRNA has been recently completed, providing an excellent platform to analyze the function of these modifications in RNA metabolism and in cellular physiology. Remarkably, majority of the rRNA modifications and the enzymatic machineries discovered in yeast are highly conserved in eukaryotes including humans. Mutations in factors involved in rRNA modification are linked to several rare severe human diseases (e.g., X-linked Dyskeratosis congenita, the Bowen–Conradi syndrome and the William–Beuren disease). In this chapter, we summarize all rRNA modifications and the corresponding enzymatic machineries of the budding yeast.

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Gao, Haixiao, Jamie Le Barron y Joachim Frank. "Ribosomal Dynamics: Intrinsic Instability of a Molecular Machine". En Non-Protein Coding RNAs, 303–16. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-70840-7_15.

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Yang, Jun, Peter Watzinger y Sunny Sharma. "Mapping of the Chemical Modifications of rRNAs". En Ribosome Biogenesis, 181–97. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_11.

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AbstractCellular RNAs, both coding and noncoding, contain several chemical modifications. Both ribose sugars and nitrogenous bases are targeted for these chemical additions. These modifications are believed to expand the topological potential of RNA molecules by bringing chemical diversity to otherwise limited repertoire. Here, using ribosomal RNA of yeast as an example, a detailed protocol for systematically mapping various chemical modifications to a single nucleotide resolution by a combination of Mung bean nuclease protection assay and RP-HPLC is provided. Molar levels are also calculated for each modification using their UV (254 nm) molar response factors that can be used for determining the amount of modifications at different residues in other RNA molecules. The chemical nature, their precise location and quantification of modifications will facilitate understanding the precise role of these chemical modifications in cellular physiology.

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Miller, W. Allen y David P. Giedroc. "Ribosomal Frameshifting in Decoding Plant Viral RNAs". En Recoding: Expansion of Decoding Rules Enriches Gene Expression, 193–220. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-89382-2_9.

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Dillon, Lawrence S. "The 5 S Ribosomal and Other Small RNAs". En The Gene, 93–143. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4899-2007-2_3.

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Sloof, P., R. Benne y B. F. De Vries. "The Extremely Small Mitochondrial Ribosomal RNAs from Trypanosomes". En Structure and Dynamics of RNA, 253–64. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5173-3_20.

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Erdmann, V. A., T. Pieler, J. Wolters, M. Digweed, D. Vogel y R. Hartmann. "Comparative Structural and Functional Studies on Small Ribosomal RNAs". En Springer Series in Molecular Biology, 164–83. New York, NY: Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4884-2_10.

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Merkl, Philipp E., Christopher Schächner, Michael Pilsl, Katrin Schwank, Kristin Hergert, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck y Herbert Tschochner. "Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro". En Ribosome Biogenesis, 39–59. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_3.

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AbstractNuclear eukaryotic RNA polymerases (RNAPs) transcribe a chromatin template in vivo. Since the basic unit of chromatin, the nucleosome, renders the DNA largely inaccessible, RNAPs have to overcome the nucleosomal barrier for efficient RNA synthesis. Gaining mechanistical insights in the transcription of chromatin templates will be essential to understand the complex process of eukaryotic gene expression. In this article we describe the use of defined in vitro transcription systems for comparative analysis of highly purified RNAPs I–III from S. cerevisiae (hereafter called yeast) transcribing in vitro reconstituted nucleosomal templates. We also provide a protocol to study promoter-dependent RNAP I transcription of purified native 35S ribosomal RNA (rRNA) gene chromatin.

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Actas de conferencias sobre el tema "Ribosomal RNAs"

Fu, Lingjie, Meili Chen, Jiayan Wu, Jingfa Xiao y Zhewen Zhang. "Comparative analysis of RNA-seq data from polyA RNAs selection and ribosomal RNAs deletion protocol by strand-specific RNA sequencing technology". En 2014 8th International Conference on Systems Biology (ISB). IEEE, 2014. http://dx.doi.org/10.1109/isb.2014.6990734.

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Cherlin, Tess, Yi Jing y Isidore Rigoutsos. "Abstract PO-127: The short non-coding RNAs known as “ribosomal RNA-derived fragments” (rRFs) are linked to race disparities in TNBC". En Abstracts: AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; October 2-4, 2020. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7755.disp20-po-127.

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Cherlin, Tess, Rogan Magee, Yi Jing, Phillipe Loher, Venetia Pliatsika y Isidore Rigoutsos. "Abstract B077: Ribosomal RNAs are fragmented into short RNAs in a manner that depends on a person’s sex, population origin, and race: implications for health disparities and personalized medicine". En Abstracts: Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; September 20-23, 2019; San Francisco, CA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7755.disp19-b077.

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Lipovich, Leonard, Pattaraporn Thepsuwan, Anton S. Goustin, Erica L. Kleinbrink, Juan Cai, Donghong Ju y James B. Brown. "Ribosomal in-frame mis-translation of stop codons in multiple open reading frames of specific human long non-coding RNAs." En 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8983047.

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Ives, Jeffrey T., Alicia M. Pierini, Jeffrey A. Stokes, Thomas M. Wahlund, Betsy Read, James H. Bechtel y Burt V. Bronk. "Nonenzymatic microorganism identification based on ribosomal RNA". En Photonics East '99, editado por Joseph Leonelli y Mark L. Althouse. SPIE, 1999. http://dx.doi.org/10.1117/12.371268.

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Panek, Josef, Jan Hajic y David Hoksza. "Template-based prediction of ribosomal RNA secondary structure". En 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2014. http://dx.doi.org/10.1109/bibm.2014.6999394.

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Balberg, Michal, Krassimira Hristova, Margit Mau, Dominic Frigon, Henry C. Zeringue, David J. Brady, David J. Beebe y Lutgarde Raskin. "Multicolor fluorescence detection of ribosomal RNA in microchannels". En BiOS 2000 The International Symposium on Biomedical Optics, editado por Raymond P. Mariella, Jr. SPIE, 2000. http://dx.doi.org/10.1117/12.379578.

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WILLIAMSON, JAMES R. "RNA FOLDING IN RIBOSOME ASSEMBLY". En Folding and Self-Assembly of Biological Macromolecules Conference. WORLD SCIENTIFIC, 2004. http://dx.doi.org/10.1142/9789812703057_0006.

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Grierson, Patrick, Kate Lillard, Gregory Behbehani, Kelly Combs, Saumitri Bhattacharyya, Acharya Samir y Joanna Groden. "Abstract PR3: The BLM helicase facilitates RNA polymerase l-mediated ribosomal RNA transcription". En Abstracts: Second AACR International Conference on Frontiers in Basic Cancer Research--Sep 14-18, 2011; San Francisco, CA. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.fbcr11-pr3.

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Hannan, Ross, Jennifer Devlin, Katherine Hannan, Nadine Hein, Megan Bywater, Gretchen Poortinga, Don Cameron et al. "Abstract PR16: Combined inhibition of ribosome function and ribosomal RNA gene transcription cooperate to delay relapse and extend survival in MYC-driven tumors". En Abstracts: Third AACR International Conference on Frontiers in Basic Cancer Research - September 18-22, 2013; National Harbor, MD. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.fbcr13-pr16.

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Informes sobre el tema "Ribosomal RNAs"

Hubbard, J. Computer modeling 16S ribosomal RNA. Office of Scientific and Technical Information (OSTI), abril de 1990. http://dx.doi.org/10.2172/6749631.

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Kemp, P. F., S. Lee y J. LaRoche. Evaluating bacterial activity from cell-specific ribosomal RNA content measured with oligonucleotide probes. Office of Scientific and Technical Information (OSTI), enero de 1992. http://dx.doi.org/10.2172/6973949.

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Horwitz, Benjamin y Barbara Gillian Turgeon. Secondary Metabolites, Stress, and Signaling: Roles and Regulation of Peptides Produced by Non-ribosomal Peptide Synthetases. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696522.bard.

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Fungal pathogens of plants produce a diverse array of small molecules. Often referred to as secondary metabolites because they were thought to be dispensable for basic functions, they may indeed have central roles as signals for the fungal cell, and in interactions with the host. We have identified more than a dozen genes encoding nonribosomal peptide synthetases (NPS) in Cochliobolusheterostrophus, the agent of southern corn leaf blight. The aim of this project was to identify roles of these genes in stress responses and signaling. The first objective was to test a complete collection of C. heterostrophus nonribosomal peptide synthetase (NRPS)-encoding gene deletion mutant and wildtype (WT) strains for sensitivity to various agents of oxidative (ROS) and nitrosative (RNOS) stress, in vitro. The second objective and next step in this part of the project was to study the relevance of sensitivity to ROS and RNOS in the host pathogen interaction, by measuring the production of ROS and RNOS in planta, when plants are inoculated with wild type and mutant strains. A third objective was to study expression of any genes shown to be involved in sensitivity to ROS or RNOS, in vitro and in planta. Another objective was to determine if any of the genes involved in oxidative or nitrosative stress responses are regulated by components of signal transduction pathways (STP) that we have identified and to determine where mechanisms overlap. Study of the collection of nps mutants identified phenotypes relevant for virulence, development and oxidative stress resistance for two of the genes, NPS2 and NPS6. Mutants in genes related to RNOS stress have no virulence phenotypes, while some of those related to ROS stress have reduced virulence as well as developmental phenotypes, so we focused primarily on ROS stress pathways. Furthermore, the identification of NPS2 and NPS6 as encoding for NRPS responsible for siderophore biosynthesis lent a new focus to the project, regulation by Fe. We have not yet developed good methods to image ROS in planta and work in this direction is continuing. We found that NPS6 expression is repressed by Fe, responding over the physiological Fe concentration range. Studying our collection of mutants, we found that conserved MAPK and G protein signal transduction pathways are dispensable for Fe regulation of NPS6, and initiated work to identify other pathways. The transcription factor SreA is one candidate, and is responsible for part, but not all, of the control of NPS6 expression. The results of this project show that the pathogen contends with oxidative stress through several signaling pathways. Loss of the siderophore produced by Nps6 makes the fungus sensitive to oxidative stress, and decreases virulence, suggesting a central role of the ability to sequester and take up extracellular iron in the host-pathogen interaction. Siderophores, and manipulation of Fe levels, could be targets for new strategies to deal with fungal pathogens of maize and other plants.

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Taylor, Ronald C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology. Office of Scientific and Technical Information (OSTI), noviembre de 1991. http://dx.doi.org/10.2172/10108317.

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Taylor, R. C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology. Office of Scientific and Technical Information (OSTI), noviembre de 1991. http://dx.doi.org/10.2172/6057182.

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Pace, N. R. Phylogenetic analysis of hyperthermophilic natural populations using ribosomal RNA sequences. Final report, July 15, 1995--July 14, 1996. Office of Scientific and Technical Information (OSTI), junio de 1997. http://dx.doi.org/10.2172/491420.

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Elroy-Stein, Orna y Dmitry Belostotsky. Mechanism of Internal Initiation of Translation in Plants. United States Department of Agriculture, diciembre de 2010. http://dx.doi.org/10.32747/2010.7696518.bard.

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Original objectives Elucidation of PABP's role in crTMV148 IRES function in-vitro using wheat germ extract and krebs-2 cells extract. Fully achieved. Elucidation of PABP's role in crTMV148 IRES function in-vivo in Arabidopsis. Characterization of the physical interactions of PABP and other potential ITAFs with crTMV148 IRES. Partly achieved. To conduct search for additional ITAFs using different approaches and evaluate the candidates. Partly achieved. Background of the topic The power of internal translation via the activity of internal ribosomal entry site (IRES) elements allow coordinated synthesis of multiple gene products from a single transcription unit, and thereby enables to bypass the need for sequential transformation with multiple independent transgenes. The key goal of this project was to identify and analyze the IRES-trans-acting factors (ITAFs) that mediate the activity of a crucifer-infecting tobamovirus (crTMV148) IRES. The remarkable conservation of the IRES activity across the phylogenetic spectrum (yeast, plants and animals) strongly suggests that key ITAFs that mediate its activity are themselves highly conserved. Thus, crTMV148 IRES offers opportunity for elucidation of the fundamental mechanisms underlying internal translation in higher plants in order to enable its rational manipulation for the purpose of agricultural biotechnology. Major conclusions and achievements. - CrTMV IRES requires PABP for maximal activity. This conclusion was achieved by PABP depletion and reconstitution of wheat germ- and Krebs2-derived in-vitro translation assays using Arabidopsis-derived PABP2, 3, 5, 8 and yeast Pab1p. - Mutations in the internal polypurine tract of the IRES decrease the high-affinity binding of all phylogenetically divergent PABPs derived from Arabidopsis and yeast in electro mobility gel shift assays. - Mutations in the internal polypurine tract decrease IRES activity in-vivo. - The 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap. - In-vivo assembled RNPs containing proteins specifically associated with the IRES were purified from HEK293 cells using the RNA Affinity in Tandem (RAT) approach followed by their identification by mass spectroscopy. - This study yielded a list of potential protein candidates that may serve as ITAFs of crTMV148 IRES activity, among them are a/b tubulin, a/g actin, GAPDH, enolase 1, ribonuclease/angiogenin inhibitor 1, 26S proteasome subunit p45, rpSA, eEF1Bδ, and proteasome b5 subunit. Implications, both scientific and agriculture. The fact that the 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap suggests a potential joint interaction between PABP, the IRES sequence and the 3'-poly(A). This has an important scientific implication related to IRES function in general.

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Lapidot, Moshe y Vitaly Citovsky. molecular mechanism for the Tomato yellow leaf curl virus resistance at the ty-5 locus. United States Department of Agriculture, enero de 2016. http://dx.doi.org/10.32747/2016.7604274.bard.

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Tomato yellow leaf curl virus (TYLCV) is a major pathogen of tomato that causes extensive crop loss worldwide, including the US and Israel. Genetic resistance in the host plant is considered highly effective in the defense against viral infection in the field. Thus, the best way to reduce yield losses due to TYLCV is by breeding tomatoes resistant or tolerant to the virus. To date, only six major TYLCV-resistance loci, termed Ty-1 to Ty-6, have been characterized and mapped to the tomato genome. Among tomato TYLCV-resistant lines containing these loci, we have identified a major recessive quantitative trait locus (QTL) that was mapped to chromosome 4 and designated ty-5. Recently, we identified the gene responsible for the TYLCV resistance at the ty-5 locus as the tomato homolog of the gene encoding messenger RNA surveillance factor Pelota (Pelo). A single amino acid change in the protein is responsible for the resistant phenotype. Pelo is known to participate in the ribosome-recycling phase of protein biosynthesis. Our hypothesis was that the resistant allele of Pelo is a “loss-of-function” mutant, and inhibits or slows-down ribosome recycling. This will negatively affect viral (as well as host-plant) protein synthesis, which may result in slower infection progression. Hence we have proposed the following research objectives: Aim 1: The effect of Pelota on translation of TYLCV proteins: The goal of this objective is to test the effect Pelota may or may not have upon translation of TYLCV proteins following infection of a resistant host. Aim 2: Identify and characterize Pelota cellular localization and interaction with TYLCV proteins: The goal of this objective is to characterize the cellular localization of both Pelota alleles, the TYLCV-resistant and the susceptible allele, to see whether this localization changes following TYLCV infection, and to find out which TYLCV protein interacts with Pelota. Our results demonstrate that upon TYLCV-infection the resistant allele of pelota has a negative effect on viral replication and RNA transcription. It is also shown that pelota interacts with the viral C1 protein, which is the only viral protein essential for TYLCV replication. Following subcellular localization of C1 and Pelota it was found that both protein localize to the same subcellular compartments. This research is innovative and potentially transformative because the role of Peloin plant virus resistance is novel, and understanding its mechanism will lay the foundation for designing new antiviral protection strategies that target translation of viral proteins. BARD Report - Project 4953 Page 2

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Savaldi-Goldstein, Sigal y Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, diciembre de 2012. http://dx.doi.org/10.32747/2012.7699849.bard.

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Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is apparent that hormones are acting in selected cells of the plant body to regulate organ growth, and furthermore, that local cell-cell communication is an important mechanism. In this proposal our goals were to identify the global profile of translated genes in response to BR stimulation and depletion in specific tissues in Arabidopsis; determine the spatio-temporal dependency of BR response on auxin transport and signaling and construct an interactive public website that will provide an integrated analysis of the data set. Our technology incorporated cell-specific polysome isolation and sequencing using the Solexa technology. In the first aim, we generated and confirmed the specificity of novel transgenic lines expressing tagged ribosomal protein in various cell types in the Arabidopsis primary root. We next crossed these lines to lines with targeted expression of BRI1 in the bri1 background. All lines were treated with BRs for two time points. The RNA-seq of their corresponding immunopurified polysomal RNA is nearly completed and the bioinformatic analysis of the data set will be completed this year. Followed, we will construct an interactive public website (our third aim). In the second aim we started revealing how spatio-temporalBR activity impinges on auxin transport in the Arabidopsis primary root. We discovered the unexpected role of BRs in controlling the expression of specific auxin efflux carriers, post-transcriptionally (Hacham et al, 2012). We also showed that this regulation depends on the specific expression of BRI1 in the epidermis. This complex and long term effect of BRs on auxin transport led us to focus on high resolution analysis of the BR signaling per se. Taking together, our ongoing collaboration and synergistic expertise (hormone action and plant development (IL) and whole-genome scale data analysis (US)) enabled the establishment of a powerful system that will tell us how distinct cell types respond to local and systemic BR signal. BR research is of special agriculture importance since BR application and BR genetic modification have been shown to significantly increase crop yield and to play an important role in plant thermotolerance. Hence, our integrated dataset is valuable for improving crop traits without unwanted impairment of unrelated pathways, for example, establishing semi-dwarf stature to allow increased yield in high planting density, inducing erect leaves for better light capture and consequent biomass increase and plant resistance to abiotic stresses.

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