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Journal articles on the topic 'Ribosomes. Proteins Eukaryotic cells'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Albanèse, Véronique, Stefanie Reissmann, and Judith Frydman. "A ribosome-anchored chaperone network that facilitates eukaryotic ribosome biogenesis." Journal of Cell Biology 189, no. 1 (2010): 69–81. http://dx.doi.org/10.1083/jcb.201001054.

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Molecular chaperones assist cellular protein folding as well as oligomeric complex assembly. In eukaryotic cells, several chaperones termed chaperones linked to protein synthesis (CLIPS) are transcriptionally and physically linked to ribosomes and are implicated in protein biosynthesis. In this study, we show that a CLIPS network comprising two ribosome-anchored J-proteins, Jjj1 and Zuo1, function together with their partner Hsp70 proteins to mediate the biogenesis of ribosomes themselves. Jjj1 and Zuo1 have overlapping but distinct functions in this complex process involving the coordinated a

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2

Nicchitta, Christopher V., Rachel S. Lerner, Samuel B. Stephens, Rebecca D. Dodd, and Brook Pyhtila. "Pathways for compartmentalizing protein synthesis in eukaryotic cells: the template-partitioning model." Biochemistry and Cell Biology 83, no. 6 (2005): 687–95. http://dx.doi.org/10.1139/o05-147.

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mRNAs encoding signal sequences are translated on endoplasmic reticulum (ER) - bound ribosomes, whereas mRNAs encoding cytosolic proteins are translated on cytosolic ribosomes. The partitioning of mRNAs to the ER occurs by positive selection; cytosolic ribosomes engaged in the translation of signal-sequence-bearing proteins are engaged by the signal-recognition particle (SRP) pathway and subsequently trafficked to the ER. Studies have demonstrated that, in addition to the SRP pathway, mRNAs encoding cytosolic proteins can also be partitioned to the ER, suggesting that RNA partitioning in the e

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Gerbasi, Vincent R., Connie M. Weaver, Salisha Hill, David B. Friedman, and Andrew J. Link. "Yeast Asc1p and Mammalian RACK1 Are Functionally Orthologous Core 40S Ribosomal Proteins That Repress Gene Expression." Molecular and Cellular Biology 24, no. 18 (2004): 8276–87. http://dx.doi.org/10.1128/mcb.24.18.8276-8287.2004.

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ABSTRACT Translation of mRNA into protein is a fundamental step in eukaryotic gene expression requiring the large (60S) and small (40S) ribosome subunits and associated proteins. By modern proteomic approaches, we previously identified a novel 40S-associated protein named Asc1p in budding yeast and RACK1 in mammals. The goals of this study were to establish Asc1p or RACK1 as a core conserved eukaryotic ribosomal protein and to determine the role of Asc1p or RACK1 in translational control. We provide biochemical, evolutionary, genetic, and functional evidence showing that Asc1p or RACK1 is inde

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4

Remacha, Miguel, Antonio Jimenez-Diaz, Cruz Santos, et al. "Proteins P1, P2, and P0, components of the eukaryotic ribosome stalk. New structural and functional aspects." Biochemistry and Cell Biology 73, no. 11-12 (1995): 959–68. http://dx.doi.org/10.1139/o95-103.

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The eukaryoic ribosomal stalk is thought to consist of the phosphoproteins P1 and P2, which form a complex with protein P0. This complex interacts at the GTPase domain in the large subunit rRNA, overlapping the binding site of the protein L11-like eukaryotic counterpart (Saccharomyces cerevisiae protein L15 and mammalian protein LI2). An unusual pool of the dephosphorylated forms of proteins P1 and P2 is detected in eukaryotic cytoplasm, and an exchange between the proteins in the pool and on the ribosome takes place during translation. Quadruply disrupted yeast strains, carrying four inactive

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5

Yusupova, Gulnara, and Marat Yusupov. "Crystal structure of eukaryotic ribosome and its complexes with inhibitors." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1716 (2017): 20160184. http://dx.doi.org/10.1098/rstb.2016.0184.

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A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transp

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Nomura, Takaomi, Kohji Nakano, Yasushi Maki, et al. "In vitro reconstitution of the GTPase-associated centre of the archaebacterial ribosome: the functional features observed in a hybrid form with Escherichia coli 50S subunits." Biochemical Journal 396, no. 3 (2006): 565–71. http://dx.doi.org/10.1042/bj20060038.

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We cloned the genes encoding the ribosomal proteins Ph (Pyrococcus horikoshii)-P0, Ph-L12 and Ph-L11, which constitute the GTPase-associated centre of the archaebacterium Pyrococcus horikoshii. These proteins are homologues of the eukaryotic P0, P1/P2 and eL12 proteins, and correspond to Escherichia coli L10, L7/L12 and L11 proteins respectively. The proteins and the truncation mutants of Ph-P0 were overexpressed in E. coli cells and used for in vitro assembly on to the conserved domain around position 1070 of 23S rRNA (E. coli numbering). Ph-L12 tightly associated as a homodimer and bound to

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7

Melnikov, Sergey, Kasidet Manakongtreecheep, Keith Rivera, Arthur Makarenko, Darryl Pappin, and Dieter Söll. "Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia." International Journal of Molecular Sciences 19, no. 12 (2018): 4125. http://dx.doi.org/10.3390/ijms19124125.

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Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasites that reproduce asexually in an environment with alleviated natural selection, Microsporidia experience continuous genome decay that is driven by Muller’s ratchet—an evolutionary process of irreversible accumulation of deleterious mutations that lead to gene loss and the miniaturization of cellular components. Particularly, Microsporidia have remarkably smal

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Woellhaf, Michael W., Frederik Sommer, Michael Schroda, and Johannes M. Herrmann. "Proteomic profiling of the mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein." Molecular Biology of the Cell 27, no. 20 (2016): 3031–39. http://dx.doi.org/10.1091/mbc.e16-07-0513.

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Whereas the structure and function of cytosolic ribosomes are well characterized, we only have a limited understanding of the mitochondrial translation apparatus. Using SILAC-based proteomic profiling, we identified 13 proteins that cofractionated with the mitochondrial ribosome, most of which play a role in translation or ribosomal biogenesis. One of these proteins is a homologue of the bacterial ribosome-silencing factor (Rsf). This protein is generated from the composite precursor protein Atp25 upon internal cleavage by the matrix processing peptidase MPP, and in this respect, it differs fr

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Stephens, Samuel B., Rebecca D. Dodd, Joseph W. Brewer, Patrick J. Lager, Jack D. Keene, and Christopher V. Nicchitta. "Stable Ribosome Binding to the Endoplasmic Reticulum Enables Compartment-specific Regulation of mRNA Translation." Molecular Biology of the Cell 16, no. 12 (2005): 5819–31. http://dx.doi.org/10.1091/mbc.e05-07-0685.

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In eukaryotic cells, protein synthesis is compartmentalized; mRNAs encoding secretory/membrane proteins are translated on endoplasmic reticulum (ER)-bound ribosomes, whereas mRNAs encoding cytosolic proteins are translated on free ribosomes. mRNA partitioning between the two compartments occurs via positive selection: free ribosomes engaged in the translation of signal sequence-encoding mRNAs are trafficked from the cytosol to the ER. After translation termination, ER-bound ribosomes are thought to dissociate, thereby completing a cycle of mRNA partitioning. At present, the physiological basis

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Graifer, Dmitri, and Galina Karpova. "Eukaryotic protein uS19: a component of the decoding site of ribosomes and a player in human diseases." Biochemical Journal 478, no. 5 (2021): 997–1008. http://dx.doi.org/10.1042/bcj20200950.

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Proteins belonging to the universal ribosomal protein (rp) uS19 family are constituents of small ribosomal subunits, and their conserved globular parts are involved in the formation of the head of these subunits. The eukaryotic rp uS19 (previously known as S15) comprises a C-terminal extension that has no homology in the bacterial counterparts. This extension is directly implicated in the formation of the ribosomal decoding site and thereby affects translational fidelity in a manner that has no analogy in bacterial ribosomes. Another eukaryote-specific feature of rp uS19 is its essential parti

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Lykke-Andersen, Jens, and Eric J. Bennett. "Protecting the proteome: Eukaryotic cotranslational quality control pathways." Journal of Cell Biology 204, no. 4 (2014): 467–76. http://dx.doi.org/10.1083/jcb.201311103.

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The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, r

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Bürk, Jonas, Benjamin Weiche, Meike Wenk, et al. "Depletion of the Signal Recognition Particle Receptor Inactivates Ribosomes in Escherichia coli." Journal of Bacteriology 191, no. 22 (2009): 7017–26. http://dx.doi.org/10.1128/jb.00208-09.

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ABSTRACT The signal recognition particle (SRP)-dependent cotranslational targeting of proteins to the cytoplasmic membrane in bacteria or the endoplasmic reticulum membrane in eukaryotes is an essential process in most living organisms. Eukaryotic cells have been shown to respond to an impairment of the SRP pathway by (i) repressing ribosome biogenesis, resulting in decreased protein synthesis, and (ii) by increasing the expression of protein quality control mechanisms, such as chaperones and proteases. In the current study, we have analyzed how bacteria like Escherichia coli respond to a grad

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Konikkat, Salini, and John L. Woolford,. "Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast." Biochemical Journal 474, no. 2 (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

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14

Ramagopal, S. "Acidic ribosomal proteins of Dictyostelium discoideum that show electrophoretic similarity to Escherichia coli proteins L7 and L12." Biochemistry and Cell Biology 67, no. 10 (1989): 712–18. http://dx.doi.org/10.1139/o89-106.

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This study documents the presence of three acidic proteins, A1 (pI 4.95), A2 (pI 4.85), and A3 (pI 4.70), in Dictyostelium discoideum ribosomes. All three proteins showed an apparent molecular mass of 13 000 by two-dimensional, sodium dodecyl sulfate gel electrophoresis. They were selectively released by treatment of ribosomes with 50% ethanol – 1 M NH4Cl. The amino acid compositions of A1, A2, and A3 were identical and indicated a predominant amount of alanine. All the above properties are shared by Escherichia coli proteins L7 and L12 and acidic ribosomal proteins in many eukaryotes. Unlike

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15

Nadanaciva, Sashi, Keith Dillman, David F. Gebhard, Alka Shrikhande, and Yvonne Will. "High-Content Screening for Compounds That Affect mtDNA-Encoded Protein Levels in Eukaryotic Cells." Journal of Biomolecular Screening 15, no. 8 (2010): 937–48. http://dx.doi.org/10.1177/1087057110373547.

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Compounds that interfere with the synthesis of either mitochondrial DNA or mtDNA-encoded proteins reduce the levels of 13 proteins essential for oxidative phosphorylation, leading to a decrease in mitochondrial adenosine triphosphate (ATP) production. Toxicity caused by these compounds is seldom identified in 24- to 72-h cytotoxicity assays due to the low turnover rates of both mtDNA and mtDNA-encoded proteins. To address this problem, the authors developed a 96-well format, high-content screening (HCS) assay that measures, in eukaryotic cells, the level of Complex IV–subunit 1, an mtDNA-encod

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Zhou, Ye, Panagiotis L. Kastritis, Shannon E. Dougherty, et al. "Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress." Proceedings of the National Academy of Sciences 117, no. 36 (2020): 22157–66. http://dx.doi.org/10.1073/pnas.2005301117.

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Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first thr

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Ghosh, Arnab, and Natalia Shcherbik. "Cooperativity between the Ribosome-Associated Chaperone Ssb/RAC and the Ubiquitin Ligase Ltn1 in Ubiquitination of Nascent Polypeptides." International Journal of Molecular Sciences 21, no. 18 (2020): 6815. http://dx.doi.org/10.3390/ijms21186815.

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Eukaryotic cells have evolved multiple mechanisms to detect and eliminate aberrant polypeptides. Co-translational protein surveillance systems play an important role in these mechanisms. These systems include ribosome-associated protein quality control (RQC) that detects aberrant nascent chains stalled on ribosomes and promotes their ubiquitination and degradation by the proteasome, and ribosome-associated chaperone Ssb/RAC, which ensures correct nascent chain folding. Despite the known function of RQC and Ssb/ribosome-associated complex (RAC) in monitoring the quality of newly generated polyp

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Ojha, Sandeep, Sulochan Malla, and Shawn M. Lyons. "snoRNPs: Functions in Ribosome Biogenesis." Biomolecules 10, no. 5 (2020): 783. http://dx.doi.org/10.3390/biom10050783.

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Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site

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Erales, Jenny, Virginie Marchand, Baptiste Panthu, et al. "Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes." Proceedings of the National Academy of Sciences 114, no. 49 (2017): 12934–39. http://dx.doi.org/10.1073/pnas.1707674114.

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Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2′-O-methylation (2′-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2′-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2′-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2′-O-Me globally by inhibiting the rRNA methyl-transferase fibri

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Mageeney, Catherine M., and Vassie C. Ware. "Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster." Molecular Biology of the Cell 30, no. 17 (2019): 2240–53. http://dx.doi.org/10.1091/mbc.e19-02-0086.

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The functional significance of ribosome heterogeneity in development and differentiation is relatively unexplored. We present the first in vivo evidence of ribosome heterogeneity playing a role in specific mRNA translation in a multicellular eukaryote. Eukaryotic-specific ribosomal protein paralogues eRpL22 and eRpL22-like are essential in development and required for sperm maturation and fertility in Drosophila. eRpL22 and eRpL22-like roles in spermatogenesis are not completely interchangeable. Flies depleted of eRpL22 and rescued by eRpL22-like overexpression have reduced fertility, confirmi

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Sattlegger, Evelyn, та Alan G. Hinnebusch. "Polyribosome Binding by GCN1 Is Required for Full Activation of Eukaryotic Translation Initiation Factor 2α Kinase GCN2 during Amino Acid Starvation". Journal of Biological Chemistry 280, № 16 (2005): 16514–21. http://dx.doi.org/10.1074/jbc.m414566200.

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The protein kinase GCN2 mediates translational control of gene expression in amino acid-starved cells by phosphorylating eukaryotic translation initiation factor 2α. InSaccharomyces cerevisiae,activation of GCN2 by uncharged tRNAs in starved cells requires its direct interaction with both the GCN1·GCN20 regulatory complex and ribosomes. GCN1 also interacts with ribosomes in cell extracts, but it was unknown whether this activity is crucial for its ability to stimulate GCN2 function in starved cells. We describe point mutations in two conserved, noncontiguous segments of GCN1 that lead to reduc

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Pusnik, Mascha, Ian Small, Laurie K. Read, Thomas Fabbro, and André Schneider. "Pentatricopeptide Repeat Proteins in Trypanosoma brucei Function in Mitochondrial Ribosomes." Molecular and Cellular Biology 27, no. 19 (2007): 6876–88. http://dx.doi.org/10.1128/mcb.00708-07.

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ABSTRACT The pentatricopeptide repeat (PPR), a degenerate 35-amino-acid motif, defines a novel eukaryotic protein family. Plants have 400 to 500 distinct PPR proteins, whereas other eukaryotes generally have fewer than 5. The few PPR proteins that have been studied have roles in organellar gene expression, probably via direct interaction with RNA. Here we show that the parasitic protozoan Trypanosoma brucei encodes 28 distinct PPR proteins, an extraordinarily high number for a nonplant organism. A comparative analysis shows that seven out of eight selected PPR proteins are mitochondrially loca

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Mangiarotti, Giorgio, and Sara Chiaberge. "Reconstitution of Functional Eukaryotic Ribosomes fromDictyostelium discoideumRibosomal Proteins and RNA." Journal of Biological Chemistry 272, no. 32 (1997): 19682–87. http://dx.doi.org/10.1074/jbc.272.32.19682.

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Akopian, David, Kush Dalal, Kuang Shen, Franck Duong, and Shu-ou Shan. "SecYEG activates GTPases to drive the completion of cotranslational protein targeting." Journal of Cell Biology 200, no. 4 (2013): 397–405. http://dx.doi.org/10.1083/jcb.201208045.

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Signal recognition particle (SRP) and its receptor (SR) comprise a highly conserved cellular machine that cotranslationally targets proteins to a protein-conducting channel, the bacterial SecYEG or eukaryotic Sec61p complex, at the target membrane. Whether SecYEG is a passive recipient of the translating ribosome or actively regulates this targeting machinery remains unclear. Here we show that SecYEG drives conformational changes in the cargo-loaded SRP–SR targeting complex that activate it for GTP hydrolysis and for handover of the translating ribosome. These results provide the first evidenc

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Remm, Maido, Anu Remm, and Mart Ustav. "Human Papillomavirus Type 18 E1 Protein Is Translated from Polycistronic mRNA by a Discontinuous Scanning Mechanism." Journal of Virology 73, no. 4 (1999): 3062–70. http://dx.doi.org/10.1128/jvi.73.4.3062-3070.1999.

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ABSTRACT Papillomaviruses are small double-stranded DNA viruses that replicate episomally in the nuclei of infected cells. The full-length E1 protein of papillomaviruses is required for the replication of viral DNA. The viral mRNA from which the human papillomavirus type 18 E1 protein is expressed is not known. We demonstrate that in eukaryotic cells, the E1 protein is expressed from polycistronic mRNA containing E6, E7, and E1 open reading frames (ORFs). The translation of adjacent E7 and E1 ORFs is not associated; it is performed by separate populations of ribosomes. The translation of the d

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Alonso, F. J. Martinez, M. V. Toledo Lobo, S. Rodriguez Martínez, F. M. Muñoz Postigo, and J. J. López-Fando Castro. "Nuclear localization of initiation factor 2 in neuron primary cultures." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 774–75. http://dx.doi.org/10.1017/s0424820100140245.

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The dominant mechanism that controls protein synthesis is the phosphorylation/dephosphorylation of initiation and elongation factors, with a translational control function. Each phase of protein synthesis is promoted by some of these factors that transiently interact with ribosomes, mRNAs and aminoacyltRNAs. Eukaryotic initiation factor-2 (eIF2, 130 kD) is one of these proteins and it is composed of three subunits: alpha, beta and gamma. eIF2 forms a ternary complex (GTP-eIF2-Met tRNAi) that can then interact with the 40S ribosomal subunit which in turn binds mRNA and the 60S ribosomal subunit

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Wong, Chi C., David Traynor, Nicolas Basse, Robert R. Kay, and Alan J. Warren. "Defective ribosome assembly in Shwachman-Diamond syndrome." Blood 118, no. 16 (2011): 4305–12. http://dx.doi.org/10.1182/blood-2011-06-353938.

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AbstractShwachman-Diamond syndrome (SDS), a recessive leukemia predisposition disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, skeletal abnormalities and poor growth, is caused by mutations in the highly conserved SBDS gene. Here, we test the hypothesis that defective ribosome biogenesis underlies the pathogenesis of SDS. We create conditional mutants in the essential SBDS ortholog of the ancient eukaryote Dictyostelium discoideum using temperature-sensitive, self-splicing inteins, showing that mutant cells fail to grow at the restrictive temperature because ri

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Oostergetel, G. T., J. S. Wall, J. F. Hainfeld, and M. Boublik. "Conformation of Free Ribosomal RNAs by STEM and Wet Film Technique as a Phylogenetic Probe." Proceedings, annual meeting, Electron Microscopy Society of America 43 (August 1985): 498–99. http://dx.doi.org/10.1017/s0424820100119314.

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The similarity of ribosomes involvement in protein synthesis in evolutionarily distant species makes this cellular organelle an attractive phylogenetic probe. The evolutionary changes in ribosomes are reflected not only in the morphology of the ribosome but also in the composition and structure of its components - proteins and RNAs.We have investigated the extent of structural similarity of free rRNAs from baby hamster kidney (BHK) cells and Escherichia coli as examples of RNAs from a eukaryote and a prokaryote, respectively. Using dedicated STEM and “wet film” technique (Wall et al. these Pro

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Copeland, Paul R., Vincent A. Stepanik, and Donna M. Driscoll. "Insight into Mammalian Selenocysteine Insertion: Domain Structure and Ribosome Binding Properties of Sec Insertion Sequence Binding Protein 2." Molecular and Cellular Biology 21, no. 5 (2001): 1491–98. http://dx.doi.org/10.1128/mcb.21.5.1491-1498.2001.

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ABSTRACT The cotranslational incorporation of the unusual amino acid selenocysteine (Sec) into both prokaryotic and eukaryotic proteins requires the recoding of a UGA stop codon as one specific for Sec. The recognition of UGA as Sec in mammalian selenoproteins requires a Sec insertion sequence (SECIS) element in the 3′ untranslated region as well as the SECIS binding protein SBP2. Here we report a detailed analysis of SBP2 structure and function using truncation and site-directed mutagenesis. We have localized the RNA binding domain to a conserved region shared with several ribosomal proteins

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Komar, Anton A., Stephane R. Gross, Diane Barth-Baus, et al. "Novel Characteristics of the Biological Properties of the YeastSaccharomyces cerevisiaeEukaryotic Initiation Factor 2A." Journal of Biological Chemistry 280, no. 16 (2005): 15601–11. http://dx.doi.org/10.1074/jbc.m413728200.

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Eukaryotic initiation factor 2A (eIF2A) has been shown to direct binding of the initiator methionyl-tRNA (Met-tRNAi) to 40 S ribosomal subunits in a codon-dependent manner, in contrast to eIF2, which requires GTP but not the AUG codon to bind initiator tRNA to 40 S subunits. We show here that yeast eIF2A genetically interacts with initiation factor eIF4E, suggesting that both proteins function in the same pathway. The doubleeIF2A/eIF4E-tsmutant strain displays a severe slow growth phenotype, which correlated with the accumulation of 85% of the double mutant cells arrested at the G2/M border. T

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Moy, Terence I., and Pamela A. Silver. "Requirements for the nuclear export of the small ribosomal subunit." Journal of Cell Science 115, no. 14 (2002): 2985–95. http://dx.doi.org/10.1242/jcs.115.14.2985.

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Eukaryotic ribosome biogenesis requires multiple steps of nuclear transport because ribosomes are assembled in the nucleus while protein synthesis occurs in the cytoplasm. Using an in situ RNA localization assay in the yeast Saccharomyces cerevisiae, we determined that efficient nuclear export of the small ribosomal subunit requires Yrb2, a factor involved in Crm1-mediated export. Furthermore, in cells lacking YRB2, the stability and abundance of the small ribosomal subunit is decreased in comparison with the large ribosomal subunit. To identify additional factors affecting small subunit expor

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Srivastava, Leena, Yevgeniya R. Lapik, Minshi Wang, and Dimitri G. Pestov. "Mammalian DEAD Box Protein Ddx51 Acts in 3′ End Maturation of 28S rRNA by Promoting the Release of U8 snoRNA." Molecular and Cellular Biology 30, no. 12 (2010): 2947–56. http://dx.doi.org/10.1128/mcb.00226-10.

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ABSTRACT Biogenesis of eukaryotic ribosomes requires a number of RNA helicases that drive molecular rearrangements at various points of the assembly pathway. While many ribosome synthesis factors are conserved among all eukaryotes, certain features of ribosome maturation, such as U8 snoRNA-assisted processing of the 5.8S and 28S rRNA precursors, are observed only in metazoan cells. Here, we identify the mammalian DEAD box helicase family member Ddx51 as a novel ribosome synthesis factor and an interacting partner of the nucleolar GTP-binding protein Nog1. Unlike any previously studied yeast he

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Si, Kausik, and Umadas Maitra. "The Saccharomyces cerevisiae Homologue of Mammalian Translation Initiation Factor 6 Does Not Function as a Translation Initiation Factor." Molecular and Cellular Biology 19, no. 2 (1999): 1416–26. http://dx.doi.org/10.1128/mcb.19.2.1416.

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ABSTRACT Eukaryotic translation initiation factor 6 (eIF6) binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. The Saccharomyces cerevisiae gene that encodes the 245-amino-acid eIF6 (calculated M r 25,550), designated TIF6, has been cloned and expressed inEscherichia coli. The purified recombinant protein prevents association between 40S and 60S ribosomal subunits to form 80S ribosomes. TIF6 is a single-copy gene that maps on chromosome XVI and is essential for cell growth. eIF6 expressed in yeast cells associates with free 60S ribosomal subunits but

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Ohnishi, Makoto, Laszlo Janosi, Masahiro Shuda, et al. "Molecular Cloning, Sequencing, Purification, and Characterization of Pseudomonas aeruginosa Ribosome Recycling Factor." Journal of Bacteriology 181, no. 4 (1999): 1281–91. http://dx.doi.org/10.1128/jb.181.4.1281-1291.1999.

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ABSTRACT Ribosome recycling factor (RRF) is required for release of 70S ribosomes from mRNA on reaching the termination codon for the next cycle of protein synthesis. The RRF-encoding gene (frr) ofPseudomonas aeruginosa PAO1 was functionally cloned by using a temperature-sensitive frr mutant ofEscherichia coli and sequenced. The P. aeruginosa frr was mapped at 30 to 32 min of the P. aeruginosachromosome. The deduced amino acid sequence of RRF showed a 64% identity to that of E. coli RRF. In an assay includingE. coli polysome and elongation factor G, purified recombinant RRF of P. aeruginosa re

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Björkholm, Patrik, Ajith Harish, Erik Hagström, Andreas M. Ernst, and Siv G. E. Andersson. "Mitochondrial genomes are retained by selective constraints on protein targeting." Proceedings of the National Academy of Sciences 112, no. 33 (2015): 10154–61. http://dx.doi.org/10.1073/pnas.1421372112.

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Mitochondria are energy-producing organelles in eukaryotic cells considered to be of bacterial origin. The mitochondrial genome has evolved under selection for minimization of gene content, yet it is not known why not all mitochondrial genes have been transferred to the nuclear genome. Here, we predict that hydrophobic membrane proteins encoded by the mitochondrial genomes would be recognized by the signal recognition particle and targeted to the endoplasmic reticulum if they were nuclear-encoded and translated in the cytoplasm. Expression of the mitochondrially encoded proteins Cytochrome oxi

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Ries, Fabian, Claudia Herkt, and Felix Willmund. "Co-Translational Protein Folding and Sorting in Chloroplasts." Plants 9, no. 2 (2020): 214. http://dx.doi.org/10.3390/plants9020214.

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Cells depend on the continuous renewal of their proteome composition during the cell cycle and in order to replace aberrant proteins or to react to changing environmental conditions. In higher eukaryotes, protein synthesis is achieved by up to five million ribosomes per cell. With the fast kinetics of translation, the large number of newly made proteins generates a substantial burden for protein homeostasis and requires a highly orchestrated cascade of factors promoting folding, sorting and final maturation. Several of the involved factors directly bind to translating ribosomes for the early p

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Kappel, Lisa, Mathias Loibl, Gertrude Zisser, et al. "Rlp24 activates the AAA-ATPase Drg1 to initiate cytoplasmic pre-60S maturation." Journal of Cell Biology 199, no. 5 (2012): 771–82. http://dx.doi.org/10.1083/jcb.201205021.

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Formation of eukaryotic ribosomes is driven by energy-consuming enzymes. The AAA-ATPase Drg1 is essential for the release of several shuttling proteins from cytoplasmic pre-60S particles and the loading of late joining proteins. However, its exact role in ribosome biogenesis has been unknown. Here we show that the shuttling protein Rlp24 recruited Drg1 to pre-60S particles and stimulated its ATPase activity. ATP hydrolysis in the second AAA domain of Drg1 was required to release shuttling proteins. In vitro, Drg1 specifically and exclusively extracted Rlp24 from purified pre-60S particles. Rlp

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GRAIFER, Dmitri, Maxim MOLOTKOV, Anna EREMINA, Aliya VEN'YAMINOVA, Marina REPKOVA, and Galina KARPOVA. "The central part of the 5.8 S rRNA is differently arranged in programmed and free human ribosomes." Biochemical Journal 387, no. 1 (2005): 139–45. http://dx.doi.org/10.1042/bj20041450.

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A sequence-specific modification of the human 5.8 S rRNA in isolated 60 S subunits, non-programmed 80 S ribosomes and ribosomes complexed with mRNA and tRNAs was studied with the use of a derivative of the nonaribonucleotide UCUGUGUUU bearing a perfluorophenylazide group on the C-5 atom of the 5′-terminal uridine. Part of the oligonucleotide moiety of the derivative was complementary to the 5.8 S rRNA sequence ACACA in positions 82–86 flanked by two guanines at the 5′-terminus. The target for the cross-linking was identified as nucleotide G89 on the 5.8 S RNA. In addition, several ribosomal pr

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Melnikov, Sergey, Hui-Si Kwok, Kasidet Manakongtreecheep, Antonia van den Elzen, Carson C. Thoreen, and Dieter Söll. "Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus." Molecular Biology and Evolution 37, no. 1 (2019): 124–33. http://dx.doi.org/10.1093/molbev/msz207.

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Abstract Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as features unique to eukaryotic proteins, we show here that similar or identical protein segments are present in ribosomal proteins from the Archaea. Specifically, the ribosomal proteins uL3, uL15, uL18, and uS12 possess NLS-type motifs that are conserved across all major branches of the Archaea, including the most ancient groups Microarchaeota and Diapherotrit

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Pawar, Vidya, Antara De, Laura Briggs, et al. "RNAi Screening of Drosophila (Sophophora) melanogaster S2 Cells for Ricin Sensitivity and Resistance." Journal of Biomolecular Screening 16, no. 4 (2011): 436–42. http://dx.doi.org/10.1177/1087057110397890.

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The ribosome-inhibiting toxin ricin binds exposed β1→4 linked galactosyls on multiple glycolipids and glycoproteins on the cell surface of most eukaryotic cells. After endocytosis, internal cell trafficking is promiscuous, with only a small proportion of ricin proceeding down a productive (cytotoxic) trafficking route to the endoplasmic reticulum (ER). Here, the catalytic ricin A chain traverses the membrane to inactivate the cytosolic ribosomes, which can be monitored by measuring reduction in protein biosynthetic capacity or cell viability. Although some markers have been discovered for the

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Hock, Daniella H., David R. L. Robinson, and David A. Stroud. "Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome." Biochemical Journal 477, no. 21 (2020): 4085–132. http://dx.doi.org/10.1042/bcj20190767.

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Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1–F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indee

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Sugiyama, Hayami, Kazutoshi Takahashi, Takuya Yamamoto, et al. "Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells." Proceedings of the National Academy of Sciences 114, no. 2 (2016): 340–45. http://dx.doi.org/10.1073/pnas.1617234114.

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Novel APOBEC1 target 1 (Nat1) (also known as “p97,” “Dap5,” and “Eif4g2”) is a ubiquitously expressed cytoplasmic protein that is homologous to the C-terminal two thirds of eukaryotic translation initiation factor 4G (Eif4g1). We previously showed that Nat1-null mouse embryonic stem cells (mES cells) are resistant to differentiation. In the current study, we found that NAT1 and eIF4G1 share many binding proteins, such as the eukaryotic translation initiation factors eIF3 and eIF4A and ribosomal proteins. However, NAT1 did not bind to eIF4E or poly(A)-binding proteins, which are critical for ca

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Stephens, Samuel B., and Christopher V. Nicchitta. "Divergent Regulation of Protein Synthesis in the Cytosol and Endoplasmic Reticulum Compartments of Mammalian Cells." Molecular Biology of the Cell 19, no. 2 (2008): 623–32. http://dx.doi.org/10.1091/mbc.e07-07-0677.

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In eukaryotic cells, mRNAs encoding signal sequence-bearing proteins undergo translation-dependent trafficking to the endoplasmic reticulum (ER), thereby restricting secretory and integral membrane protein synthesis to the ER compartment. However, recent studies demonstrating that mRNAs encoding cytosolic/nucleoplasmic proteins are represented on ER-bound polyribosomes suggest a global role for the ER in cellular protein synthesis. Here, we examined the steady-state protein synthesis rates and compartmental distribution of newly synthesized proteins in the cytosol and ER compartments. We repor

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Pavitt, Graham D., and Christopher G. Proud. "Protein synthesis and its control in neuronal cells with a focus on vanishing white matter disease." Biochemical Society Transactions 37, no. 6 (2009): 1298–310. http://dx.doi.org/10.1042/bst0371298.

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Protein synthesis (also termed mRNA translation) is a key step in the expression of a cell's genetic information, in which the information contained within the coding region of the mRNA is used to direct the synthesis of the new protein, a process that is catalysed by the ribosome. Protein synthesis must be tightly controlled, to ensure the right proteins are made in the right amounts at the right time, and must be accurate, to avoid errors that could lead to the production of defective and potentially damaging proteins. In addition to the ribosome, protein synthesis also requires proteins ter

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Ude, Susanne, Jürgen Lassak, Agata L. Starosta, Tobias Kraxenberger, Daniel N. Wilson, and Kirsten Jung. "Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches." Science 339, no. 6115 (2012): 82–85. http://dx.doi.org/10.1126/science.1228985.

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Translation elongation factor P (EF-P) is critical for virulence in bacteria. EF-P is present in all bacteria and orthologous to archaeal and eukaryotic initiation factor 5A, yet the biological function has so far remained enigmatic. Here, we demonstrate that EF-P is an elongation factor that enhances translation of polyproline-containing proteins: In the absence of EF-P, ribosomes stall at polyproline stretches, whereas the presence of EF-P alleviates the translational stalling. Moreover, we demonstrate the physiological relevance of EF-P to fine-tune the expression of the polyproline-contain

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Andreev, Dmitri E., Ilya M. Terenin, Yan E. Dunaevsky, Sergei E. Dmitriev, and Ivan N. Shatsky. "A Leaderless mRNA Can Bind to Mammalian 80S Ribosomes and Direct Polypeptide Synthesis in the Absence of Translation Initiation Factors." Molecular and Cellular Biology 26, no. 8 (2006): 3164–69. http://dx.doi.org/10.1128/mcb.26.8.3164-3169.2006.

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ABSTRACT Translation initiation in eukaryotic cells is known to be a complex multistep process which involves numerous protein factors. Here we demonstrate that leaderless mRNAs with initiator Met-tRNA can bind directly to 80S mammalian ribosomes in the absence of initiation factors and that the complexes thus formed are fully competent for the subsequent steps of polypeptide synthesis. We show that the canonical 48S pathway of eukaryotic translation initiation has no obvious advantage over the 80S pathway of translation initiation on leaderless mRNAs and suggest that, in the presence of compe

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Ripmaster, T. L., G. P. Vaughn, and J. L. Woolford. "DRS1 to DRS7, novel genes required for ribosome assembly and function in Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 12 (1993): 7901–12. http://dx.doi.org/10.1128/mcb.13.12.7901-7912.1993.

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To identify Saccharomyces cerevisiae mutants defective in assembly or function of ribosomes, a collection of cold-sensitive strains generated by treatment with ethyl methanesulfonate was screened by sucrose gradient analysis for altered ratios of free 40S to 60S ribosomal subunits or qualitative changes in polyribosome profiles. Mutations defining seven complementation groups deficient in ribosomal subunits, drs1 to drs7, were identified. We have previously shown that DRS1 encodes a putative ATP-dependent RNA helicase necessary for assembly of 60S ribosomal subunits (T. L. Ripmaster, G. P. Vau

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Mohan, Jagan, and Thomas Wollert. "Human ubiquitin-like proteins as central coordinators in autophagy." Interface Focus 8, no. 5 (2018): 20180025. http://dx.doi.org/10.1098/rsfs.2018.0025.

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Autophagy is one of the most versatile recycling systems of eukaryotic cells. It degrades diverse cytoplasmic components such as organelles, protein aggregates, ribosomes and multi-enzyme complexes. Not surprisingly, any failure of autophagy or reduced activity of the pathway contributes to the onset of various pathologies, including neurodegeneration, cancer and metabolic disorders such as diabetes or immune diseases. Furthermore, autophagy contributes to the innate immune response and combats bacterial or viral pathogens. The hallmark of macroautophagy is the formation of a membrane sack tha

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Zou, Meijuan, Ying Mu, Xin Chai, et al. "The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development." Nucleic Acids Research 48, no. 6 (2020): 3195–210. http://dx.doi.org/10.1093/nar/gkaa129.

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Abstract Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. The formation of methylated nucleotides is performed by a variety of RNA-methyltransferases. Chloroplasts of plant cells result from an endosymbiotic event and possess their own genome and ribosomes. However, enzymes responsible for rRNA methylation and the function of modified nucleotides in chloroplasts remain to be determined. Here, we identified an rRNA methyltransferase, CMAL (Chloroplast MraW-Like), in the Arabidopsis chloroplast and investigated its function. CMAL i

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Pavlova, Julia A., Zimfira Z. Khairullina, Andrey G. Tereshchenkov, et al. "Triphenilphosphonium Analogs of Chloramphenicol as Dual-Acting Antimicrobial and Antiproliferating Agents." Antibiotics 10, no. 5 (2021): 489. http://dx.doi.org/10.3390/antibiotics10050489.

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In the current work, in continuation of our recent research, we synthesized and studied new chimeric compounds, including the ribosome-targeting antibiotic chloramphenicol (CHL) and the membrane-penetrating cation triphenylphosphonium (TPP), which are linked by alkyl groups of different lengths. Using various biochemical assays, we showed that these CAM-Cn-TPP compounds bind to the bacterial ribosome, inhibit protein synthesis in vitro and in vivo in a way similar to that of the parent CHL, and significantly reduce membrane potential. Similar to CAM-C4-TPP, the mode of action of CAM-C10-TPP an

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