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Автор: Grafiati

Опубліковано: 6 вересня 2023

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1

Ramirez, Celia, Lawrence C. Shimmin, C. Hunter Newton, Alastair T. Matheson, and Patrick P. Dennis. "Structure and evolution of the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 234–44. http://dx.doi.org/10.1139/m89-036.

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The genes corresponding to the L11, L1, L10, and L12 equivalent ribosomal proteins (L11e, L1e, L10e, and L12e) of Escherichia coli have been cloned and sequenced from two widely divergent species of archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus, and the L10 and four different L12 genes have been cloned and sequenced from the eucaryote Saccharomyces cerevisiae. Alignments between the deduced amino acid sequences of these proteins and to other available homologous proteins of eubacteria and eucaryotes have been made. The data suggest that the archaebacteria are a distinct coherent phylogenetic group. Alignment of the proline-rich L11e proteins reveals that the N-terminal region, believed to be responsible for interaction with release factor 1, is the most highly conserved region and that there is specific conservation of most of the proline residues, which may be important in maintaining the highly elongated structure of the molecule. Although L11 is the most highly methylated protein in the E. coli ribosome, the sites of methylation are not conserved in the archaebacterial L11e proteins. The L1e proteins of eubacteria and archaebacteria show two regions of very high similarity near the center and the carboxy termini of the proteins. The L10e proteins of all kingdoms are colinear and contain approximately three fourths of an L12e protein fused to their carboxy terminus, although much of this fusion has been lost in the truncated eubacterial protein. The archaebacterial and eucaryotic L12e proteins are colinear, whereas the eubacterial protein has suffered a rearrangement through what appear to be gene fusion events. Within the L12e derived region of the L10e proteins there exists a repeated module of 26 amino acids, present in two copies in eucaryotes, three in archaebacteria, and one in eubacteria. This modular sequence is apparently also present in the L12e proteins of all kingdoms and may play a role in L12e dimerization, L10e–L12e complex formation, and the function of the L10e–L12e complex in translation.Key words: translation, ribosome.

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2

Mitroshin, Ivan, Maria Garber, and Azat Gabdulkhakov. "Crystallographic analysis of archaeal ribosomal protein L11." Acta Crystallographica Section F Structural Biology Communications 71, no. 8 (July 29, 2015): 1083–87. http://dx.doi.org/10.1107/s2053230x15011395.

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Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. L11 is a highly conserved two-domain ribosomal protein. The C-terminal domain of L11 is an RNA-binding domain that binds to a fragment of 23S rRNA and stabilizes its structure. The complex between L11 and 23S rRNA is involved in the GTPase activity of the translation elongation and release factors. Bacterial and archaeal L11–rRNA complexes are targets for peptide antibiotics of the thiazole class. To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein. Here, the crystallization and X-ray analysis of the ribosomal protein L11 fromMethanococcus jannaschiiare reported. Crystals of the native protein and its selenomethionine derivative belonged to the orthorhombic space groupI222 and were suitable for structural studies. Native and single-wavelength anomalous dispersion data sets have been collected and determination of the structure is in progress.

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3

Yang, Xiaoming, and Edward E. Ishiguro. "Involvement of the N Terminus of Ribosomal Protein L11 in Regulation of the RelA Protein of Escherichia coli." Journal of Bacteriology 183, no. 22 (November 15, 2001): 6532–37. http://dx.doi.org/10.1128/jb.183.22.6532-6537.2001.

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ABSTRACT Amino acid-deprived rplK (previously known asrelC) mutants of Escherichia coli cannot activate (p)ppGpp synthetase I (RelA) and consequently exhibit relaxed phenotypes. The rplK gene encodes ribosomal protein L11, suggesting that L11 is involved in regulating the activity of RelA. To investigate the role of L11 in the stringent response, a derivative ofrplK encoding L11 lacking the N-terminal 36 amino acids (designated ′L11) was constructed. Bacteria overexpressing ′L11 exhibited a relaxed phenotype, and this was associated with an inhibition of RelA-dependent (p)ppGpp synthesis during amino acid deprivation. In contrast, bacteria overexpressing normal L11 exhibited a typical stringent response. The overexpressed ′L11 was incorporated into ribosomes and had no effect on the ribosome-binding activity of RelA. By several methods (yeast two-hybrid, affinity blotting, and copurification), no direct interaction was observed between the C-terminal ribosome-binding domain of RelA and L11. To determine whether the proline-rich helix of L11 was involved in RelA regulation, the Pro-22 residue was replaced with Leu by site-directed mutagenesis. The overexpression of the Leu-22 mutant derivative of L11 resulted in a relaxed phenotype. These results indicate that the proline-rich helix in the N terminus of L11 is involved in regulating the activity of RelA.

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4

Cameron, Dale M., Steven T. Gregory, Jill Thompson, Moo-Jin Suh, Patrick A. Limbach, and Albert E. Dahlberg. "Thermus thermophilus L11 Methyltransferase, PrmA, Is Dispensable for Growth and Preferentially Modifies Free Ribosomal Protein L11 Prior to Ribosome Assembly." Journal of Bacteriology 186, no. 17 (September 1, 2004): 5819–25. http://dx.doi.org/10.1128/jb.186.17.5819-5825.2004.

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ABSTRACT The ribosomal protein L11 in bacteria is posttranslationally trimethylated at multiple amino acid positions by the L11 methyltransferase PrmA, the product of the prmA gene. The role of L11 methylation in ribosome function or assembly has yet to be determined, although the deletion of Escherichia coli prmA has no apparent phenotype. We have constructed a mutant of the extreme thermophile Thermus thermophilus in which the prmA gene has been disrupted with the htk gene encoding a heat-stable kanamycin adenyltransferase. This mutant shows no growth defects, indicating that T. thermophilus PrmA, like its E. coli homolog, is dispensable. Ribosomes prepared from this mutant contain unmethylated L11, as determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and are effective substrates for in vitro methylation by cloned and purified T. thermophilus PrmA. MALDI-TOF MS also revealed that T. thermophilus L11 contains a total of 12 methyl groups, in contrast to the 9 methyl groups found in E. coli L11. Finally, we found that, as with the E. coli methyltransferase, the ribosomal protein L11 dissociated from ribosomes is a more efficient substrate for in vitro methylation by PrmA than intact 70S ribosomes, suggesting that methylation in vivo occurs on free L11 prior to its incorporation into ribosomes.

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5

Bailly, Christian, and Gérard Vergoten. "Interaction of Camptothecin Anticancer Drugs with Ribosomal Proteins L15 and L11: A Molecular Docking Study." Molecules 28, no. 4 (February 15, 2023): 1828. http://dx.doi.org/10.3390/molecules28041828.

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The antitumor drug topotecan (TPT) is a potent inhibitor of topoisomerase I, triggering DNA breaks lethal for proliferating cancer cells. The mechanism is common to camptothecins SN38 (the active metabolite of irinotecan) and belotecan (BLT). Recently, TPT was shown to bind the ribosomal protein L15, inducing an antitumor immune activation independent of topoisomerase I. We have modeled the interaction of four camptothecins with RPL15 derived from the 80S human ribosome. Two potential drug-binding sites were identified at Ile135 and Phe129. SN38 can form robust RPL15 complexes at both sites, whereas BLT essentially gave stable complexes with site Ile135. The empirical energy of interaction (ΔE) for SN38 binding to RPL15 is similar to that determined for TPT binding to the topoisomerase I-DNA complex. Molecular models with the ribosomal protein L11 sensitive to topoisomerase inhibitors show that SN38 can form a robust complex at a single site (Cys25), much more stable than those with TPT and BLT. The main camptothecin structural elements implicated in the ribosomal protein interaction are the lactone moiety, the aromatic system and the 10-hydroxyl group. The study provides guidance to the design of modulators of ribosomal proteins L11 and L15, both considered anticancer targets.

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6

Remacha, Miguel, Antonio Jimenez-Diaz, Cruz Santos, Elisa Briones, Reina Zambrano, M. A. Rodriguez Gabriel, E. Guarinos, and Juan P. G. Ballesta. "Proteins P1, P2, and P0, components of the eukaryotic ribosome stalk. New structural and functional aspects." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 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 acidic protein genes and, therefore, containing ribosomes totally depleted of acidic proteins, are viable but grow with a doubling time threefold higher than wild-type cells. The in vitro translation systems derived from these stains are active but the two-dimensional gel electrophoresis pattern of proteins expressed in vivo and in vitro is partially different. These results indicate that the P1 and P2 proteins are not essential for ribosome activity but are able to affect the translation of some specific mRNAs. Protein P0 is analogous to bacterial ribosomal protein L10 but carries an additional carboxyl domain showing a high sequence homology to the acidic proteins P1 and P2, including the terminal peptide DDDMGFGLFD. Successive deletions of the P0 carboxyl domain show that removal of the last 21 amino acids from the P0 carboxyl domain only slightly affects the ribosome activity in a wild-type genetic background; however, the same deletion is lethal in a quadruple disruptant deprived of acidic P1/P2 proteins. Additional deletions affect the interaction of P0 with the P1 and P2 proteins and with the rRNA. The experimental data available support the implication of the eukaryotic stalk components in some regulatory process that modulates the ribosomal activity.Key words: ribosomal stalk, acidic proteins, phosphorylation, GTPase domain, translation regulation.

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7

Kraft, Alexander, Christina Lutz, Arno Lingenhel, Peter Gröbner, and Wolfgang Piendl. "Control of Ribosomal Protein L1 Synthesis in Mesophilic and Thermophilic Archaea." Genetics 152, no. 4 (August 1, 1999): 1363–72. http://dx.doi.org/10.1093/genetics/152.4.1363.

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Abstract The mechanisms for the control of ribosomal protein synthesis have been characterized in detail in Eukarya and in Bacteria. In Archaea, only the regulation of the MvaL1 operon (encoding ribosomal proteins MvaL1, MvaL10, and MvaL12) of the mesophilic Methanococcus vannielii has been extensively investigated. As in Bacteria, regulation takes place at the level of translation. The regulator protein MvaL1 binds preferentially to its binding site on the 23S rRNA, and, when in excess, binds to the regulatory target site on its mRNA and thus inhibits translation of all three cistrons of the operon. The regulatory binding site on the mRNA, a structural mimic of the respective binding site on the 23S rRNA, is located within the structural gene about 30 nucleotides downstream of the ATG start codon. MvaL1 blocks a step before or at the formation of the first peptide bond of MvaL1. Here we demonstrate that a similar regulatory mechanism exists in the thermophilic M. thermolithotrophicus and M. jannaschii. The L1 gene is cotranscribed together with the L10 and L11 gene, in all genera of the Euryarchaeota branch of the Archaea studied so far. A potential regulatory L1 binding site located within the structural gene, as in Methanococcus, was found in Methanobacterium thermoautotrophicum and in Pyrococcus horikoshii. In contrast, in Archaeoglobus fulgidus a typical L1 binding site is located in the untranslated leader of the L1 gene as described for the halophilic Archaea. In Sulfolobus, a member of the Crenarchaeota, the L1 gene is part of a long transcript (encoding SecE, NusG, L11, L1, L10, L12). A previously suggested regulatory L1 target site located within the L11 structural gene could not be confirmed as an L1 binding site.

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8

Liao, Daiqing, and Patrick P. Dennis. "Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences." Journal of Molecular Evolution 38, no. 4 (April 1994): 405–19. http://dx.doi.org/10.1007/bf00163157.

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9

Zhang, Yanping, Gabrielle White Wolf, Krishna Bhat, Aiwen Jin, Theresa Allio, William A. Burkhart, and Yue Xiong. "Ribosomal Protein L11 Negatively Regulates Oncoprotein MDM2 and Mediates a p53-Dependent Ribosomal-Stress Checkpoint Pathway." Molecular and Cellular Biology 23, no. 23 (December 1, 2003): 8902–12. http://dx.doi.org/10.1128/mcb.23.23.8902-8912.2003.

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ABSTRACT The gene encoding p53 mediates a major tumor suppression pathway that is frequently altered in human cancers. p53 function is kept at a low level during normal cell growth and is activated in response to various cellular stresses. The MDM2 oncoprotein plays a key role in negatively regulating p53 activity by either direct repression of p53 transactivation activity in the nucleus or promotion of p53 degradation in the cytoplasm. DNA damage and oncogenic insults, the two best-characterized p53-dependent checkpoint pathways, both activate p53 through inhibition of MDM2. Here we report that the human homologue of MDM2, HDM2, binds to ribosomal protein L11. L11 binds a central region in HDM2 that is distinct from the ARF binding site. We show that the functional consequence of L11-HDM2 association, like that with ARF, results in the prevention of HDM2-mediated p53 ubiquitination and degradation, subsequently restoring p53-mediated transactivation, accumulating p21 protein levels, and inducing a p53-dependent cell cycle arrest by canceling the inhibitory function of HDM2. Interference with ribosomal biogenesis by a low concentration of actinomycin D is associated with an increased L11-HDM2 interaction and subsequent p53 stabilization. We suggest that L11 functions as a negative regulator of HDM2 and that there might exist in vivo an L11-HDM2-p53 pathway for monitoring ribosomal integrity.

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10

Zhang, Shuyu, Janelle M. Scott та W. G. Haldenwang. "Loss of Ribosomal Protein L11 Blocks Stress Activation of the Bacillus subtilis Transcription Factor ςB". Journal of Bacteriology 183, № 7 (1 квітня 2001): 2316–21. http://dx.doi.org/10.1128/jb.183.7.2316-2321.2001.

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ABSTRACT ςB, the general stress response sigma factor ofBacillus subtilis, is activated when the cell's energy levels decline or the bacterium is exposed to environmental stress (e.g., heat shock, ethanol). Physical stress activates ςBthrough a collection of regulatory kinases and phosphatases (the Rsb proteins) which catalyze the release of ςB from an anti-ςB factor inhibitor. The means by which diverse stresses communicate with the Rsb proteins is unknown; however, a role for the ribosome in this process was suggested when several of the upstream members of the ςB stress activation cascade (RsbR, -S, and -T) were found to cofractionate with ribosomes in crudeB. subtilis extracts. We now present evidence for the involvement of a ribosome-mediated process in the stress activation of ςB. B. subtilis strains resistant to the antibiotic thiostrepton, due to the loss of ribosomal protein L11 (RplK), were found to be blocked in the stress activation of ςB. Neither the energy-responsive activation of ςB nor stress-dependent chaperone gene induction (a ςB-independent stress response) was inhibited by the loss of L11. The Rsb proteins required for stress activation of ςB are shown to be active in the RplK−strain but fail to be triggered by stress. The data demonstrate that the B. subtilis ribosomes provide an essential input for the stress activation of ςB and suggest that the ribosomes may themselves be the sensors for stress in this system.

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11

Katsani, K. R., P. Tsiboli, K. Anagnostopoulos, H. Urlaub, and T. Choli-Papadopoulou. "Identification of the 50S Ribosomal Proteins from the Eubacterium Thermus thermophilus." Biological Chemistry 381, no. 11 (November 15, 2000): 1079–87. http://dx.doi.org/10.1515/bc.2000.133.

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Abstract The total protein mixture from the 50S subunit (TP-50) of the eubacterium Thermus thermophilus was characterized after blotting onto PVDF membranes from two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and sequencing. The proteins were numbered according to their primary structure similarity with their counterparts from other species. One of them has been marked with an asterisk, namely L*23, because unlike the other known ribosomal proteins it shows a very low degree of homology. A highly acidic 5S rRNA binding protein, TL5, was characterized and compared with the available primary structure information. Proteins L1 and L4 migrate similarly on 2D-PAGE. Protein L4, essential for protein biosynthesis, is N-terminally blocked and shows a strikingly low homology to other L4 proteins. In addition to L4, two other proteins, namely L10 and L11, were found to be N-terminally blocked. In conclusion, 33 proteins from the large subunit were identified, including TL5. Homologs to rpL25 and rpL26 were not found.

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12

Xing, Yanyan, and David E. Draper. "Stabilization of a ribosomal RNA tertiary structure by ribosomal protein L11." Journal of Molecular Biology 249, no. 2 (January 1995): 319–31. http://dx.doi.org/10.1006/jmbi.1995.0299.

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13

Chan, Yuen-Ling, Joe Olvera, Veronica Paz, and Ira G. Wool. "The primary structure of rat ribosomal protein L11." Biochemical and Biophysical Research Communications 185, no. 1 (May 1992): 356–62. http://dx.doi.org/10.1016/s0006-291x(05)80993-3.

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14

Nomura, Takaomi, Kohji Nakano, Yasushi Maki, Takao Naganuma, Takashi Nakashima, Isao Tanaka, Makoto Kimura, Akira Hachimori, and Toshio Uchiumi. "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 (May 29, 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 the C-terminal half of Ph-P0. The Ph-P0·Ph-L12 complex and Ph-L11 bound to the 1070 rRNA fragments from the three biological kingdoms in the same manner as the equivalent proteins of eukaryotic and eubacterial ribosomes. The Ph-P0·Ph-L12 complex and Ph-L11 could replace L10·L7/L12 and L11 respectively, on the E. coli 50S subunit in vitro. The resultant hybrid ribosome was accessible for eukaryotic, as well as archaebacterial elongation factors, but not for prokaryotic elongation factors. The GTPase and polyphenylalanine-synthetic activity that is dependent on eukaryotic elongation factors was comparable with that of the hybrid ribosomes carrying the eukaryotic ribosomal proteins. The results suggest that the archaebacterial proteins, including the Ph-L12 homodimer, are functionally accessible to eukaryotic translation factors.

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15

Kim, J., J. H. Pak, W. H. Choi, J. Y. Kim, W. D. Joo, D. Y. Kim, D. S. Suh, Y. M. Kim, Y. T. Kim, and J. H. Nam. "Detection of ovarian cancer-specific gene by differentially expressed gene polymerase chain reaction prescreening and direct DNA sequencing." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 21106. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.21106.

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21106 Background: To detect the genes differentially expressed in the ovarian cancer, we analysed the genes in the ovarian cancer and normal ovary by differentially expressed gene(DEG) PCR using the RNA extracted from the both tissues. We examined the relationship between the specific genes of ovarian cancer and pathogenesis of ovarian cancer. Methods: Differentially expressed genes were screened by ACP-based PCR. Differentially expressed bands were extracted from agarose gel, and then directly sequenced. Finally we determined the clinical importances of differentially expressed genes. Results: Some genes were overexpressed in the ovarian cancer tissue than normal ovary, such as plexin B1(PLXNB1), aminoacylase 1(ACY1), solute carrier family 25 protein(SLC25A5), triosephosphate isomerase 1(TPI 1), poliovirus receptor-related 3 protein(PVRL 3), clusterin, LY6/PLAUR domain containing 1 protein(LYPDC 1). And other five genes were more expressed in the normal ovary than ovarian cancer, such as ribosomal protein L11 and L23, tenascin XB (TNXB), complement component 1 and actin alpha 2. Conclusions: Clusterin was highly expressed in the tissue from ovarian cancer, which was identified with anti- or proapoptotic activity regulated by calcium homeostasis in prostate, breast and colorectal cancers. And it suggests the possibility that regulation of clusterin activity provides the prospect of breaking down cancer cells‘ resistance to apoptosis in the ovarian cancer. Ribosomal protein L11 and L23 was highly expressed in normal ovary, which plays an important role in regulating the stability and function of the p53 tumor suppressor protein. It suggests that suppression of ribosomal protein L11 may act an important role in proliferation of ovarian cancer and over-expression of ribosomal protein L11 may act an important role in cell cycle arrest in the treatment of the ovarian cancer. No significant financial relationships to disclose.

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16

Carr, Jennifer F., Hannah J. Lee, Joshua B. Jaspers, Albert E. Dahlberg, Gerwald Jogl, and Steven T. Gregory. "Phenotypic Suppression of Streptomycin Resistance by Mutations in Multiple Components of the Translation Apparatus." Journal of Bacteriology 197, no. 18 (July 6, 2015): 2981–88. http://dx.doi.org/10.1128/jb.00219-15.

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ABSTRACTThe bacterial ribosome and its associated translation factors are frequent targets of antibiotics, and antibiotic resistance mutations have been found in a number of these components. Such mutations can potentially interact with one another in unpredictable ways, including the phenotypic suppression of one mutation by another. These phenotypic interactions can provide evidence of long-range functional interactions throughout the ribosome and its functional complexes and potentially give insights into antibiotic resistance mechanisms. In this study, we used genetics and experimental evolution of the thermophilic bacteriumThermus thermophilusto examine the ability of mutations in various components of the protein synthesis apparatus to suppress the streptomycin resistance phenotypes of mutations in ribosomal protein S12, specifically those located distant from the streptomycin binding site. With genetic selections and strain constructions, we identified suppressor mutations in EF-Tu or in ribosomal protein L11. Using experimental evolution, we identified amino acid substitutions in EF-Tu or in ribosomal proteins S4, S5, L14, or L19, some of which were found to also relieve streptomycin resistance. The wide dispersal of these mutations is consistent with long-range functional interactions among components of the translational machinery and indicates that streptomycin resistance can result from the modulation of long-range conformational signals.IMPORTANCEThe thermophilic bacteriumThermus thermophilushas become a model system for high-resolution structural studies of macromolecular complexes, such as the ribosome, while its natural competence for transformation facilitates genetic approaches. Genetic studies ofT. thermophilusribosomes can take advantage of existing high-resolution crystallographic information to allow a structural interpretation of phenotypic interactions among mutations. Using a combination of genetic selections, strain constructions, and experimental evolution, we find that certain mutations in the translation apparatus can suppress the phenotype of certain antibiotic resistance mutations. Suppression of resistance can occur by mutations located distant in the ribosome or in a translation factor. These observations suggest the existence of long-range conformational signals in the translating ribosome, particularly during the decoding of mRNA.

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17

Demirci, Hasan, Steven T. Gregory, Albert E. Dahlberg, and Gerwald Jogl. "Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA." EMBO Journal 26, no. 2 (January 11, 2007): 567–77. http://dx.doi.org/10.1038/sj.emboj.7601508.

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18

Lindström, Mikael S., Aiwen Jin, Chad Deisenroth, Gabrielle White Wolf, and Yanping Zhang. "Cancer-Associated Mutations in the MDM2 Zinc Finger Domain Disrupt Ribosomal Protein Interaction and Attenuate MDM2-Induced p53 Degradation." Molecular and Cellular Biology 27, no. 3 (November 20, 2006): 1056–68. http://dx.doi.org/10.1128/mcb.01307-06.

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ABSTRACT The p53-inhibitory function of the oncoprotein MDM2 is regulated by a number of MDM2-binding proteins, including ARF and ribosomal proteins L5, L11, and L23, which bind the central acidic domain of MDM2 and inhibit its E3 ubiquitin ligase activity. Various human cancer-associated MDM2 alterations targeting the central acidic domain have been reported, yet the functional significance of these mutations in tumor development has remained unclear. Here, we show that cancer-associated missense mutations targeting MDM2's central zinc finger disrupt the interaction of MDM2 with L5 and L11. We found that the zinc finger mutant MDM2 is impaired in undergoing nuclear export and proteasomal degradation as well as in promoting p53 degradation, yet retains the function of suppressing p53 transcriptional activity. Unlike the wild-type MDM2, whose p53-suppressive activity can be inhibited by L11, the MDM2 zinc finger mutant escapes L11 inhibition. Hence, the MDM2 central zinc finger plays a critical role in mediating MDM2's interaction with ribosomal proteins and its ability to degrade p53, and these roles are disrupted by human cancer-associated MDM2 mutations.

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19

Slomnicki, Lukasz P., Justin Hallgren, Aruna Vashishta, Scott C. Smith, Steven R. Ellis, and Michal Hetman. "Proapoptotic Requirement of Ribosomal Protein L11 in Ribosomal Stress-Challenged Cortical Neurons." Molecular Neurobiology 55, no. 1 (December 14, 2016): 538–53. http://dx.doi.org/10.1007/s12035-016-0336-y.

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20

Ishihara, Yuka, Kiyoshiro Nakamura, Shunsuke Nakagawa, Yasuhiro Okamoto, Masatatsu Yamamoto, Tatsuhiko Furukawa, and Kohichi Kawahara. "Nucleolar Stress Response via Ribosomal Protein L11 Regulates Topoisomerase Inhibitor Sensitivity of P53-Intact Cancers." International Journal of Molecular Sciences 23, no. 24 (December 15, 2022): 15986. http://dx.doi.org/10.3390/ijms232415986.

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Nucleolar stress response is caused by perturbations in ribosome biogenesis, induced by the inhibition of ribosomal RNA processing and synthesis, as well as ribosome assembly. This response induces p53 stabilization and activation via ribosomal protein L11 (RPL11), suppressing tumor progression. However, anticancer agents that kill cells via this mechanism, and their relationship with the therapeutic efficiency of these agents, remain largely unknown. Here, we sought to investigate whether topoisomerase inhibitors can induce nucleolar stress response as they reportedly block ribosomal RNA transcription. Using rhabdomyosarcoma and rhabdoid tumor cell lines that are sensitive to the nucleolar stress response, we evaluated whether nucleolar stress response is associated with sensitivity to topoisomerase inhibitors ellipticine, doxorubicin, etoposide, topotecan, and anthracyclines. Cell proliferation assay indicated that small interfering RNA-mediated RPL11 depletion resulted in decreased sensitivity to topoisomerase inhibitors. Furthermore, the expression of p53 and its downstream target proteins via western blotting showed the suppression of p53 pathway activation upon RPL11 knockdown. These results suggest that the sensitivity of cancer cells to topoisomerase inhibitors is regulated by RPL11-mediated nucleolar stress responses. Thus, RPL11 expression may contribute to the prediction of the therapeutic efficacy of topoisomerase inhibitors and increase their therapeutic effect of topoisomerase inhibitors.

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21

Dai, Mu-Shui, Hugh Arnold, Xiao-Xin Sun, Rosalie Sears, and Hua Lu. "Inhibition of c-Myc activity by ribosomal protein L11." EMBO Journal 26, no. 14 (June 28, 2007): 3332–45. http://dx.doi.org/10.1038/sj.emboj.7601776.

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22

Dai, Mu-Shui, Rosalie Sears, and Hua Lu. "Feedback Regulation of c-Myc by Ribosomal Protein L11." Cell Cycle 6, no. 22 (November 15, 2007): 2735–41. http://dx.doi.org/10.4161/cc.6.22.4895.

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23

Dai, Mu-Shui, Hugh Arnold, Xiao-Xin Sun, Rosalie Sears, and Hua Lu. "Inhibition of c-Myc activity by ribosomal protein L11." EMBO Journal 28, no. 7 (April 8, 2009): 993. http://dx.doi.org/10.1038/emboj.2009.70.

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Lohrum, Marion A. E., Robert L. Ludwig, Michael H. G. Kubbutat, Mary Hanlon, and Karen H. Vousden. "Regulation of HDM2 activity by the ribosomal protein L11." Cancer Cell 3, no. 6 (June 2003): 577–87. http://dx.doi.org/10.1016/s1535-6108(03)00134-x.

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25

BAXTER, Ross Macpherson, and Nasir ZAHID. "L16, a bifunctional ribosomal protein and the enhancing effect of L6 and L11." European Journal of Biochemistry 155, no. 2 (March 1986): 273–77. http://dx.doi.org/10.1111/j.1432-1033.1986.tb09486.x.

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26

Douthwaite, Stephen, Bjørn Voldborg, Lykke Haastrup Hansen, Gunnar Rosendahl, and Birte Vester. "Recognition determinants for proteins and antibiotics within 23S rRNA." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 1179–85. http://dx.doi.org/10.1139/o95-127.

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Ribosomal RNAs fold into phylogenetically conserved secondary and tertiary structures that determine their function in protein synthesis. We have investigated Escherichia coli 23S rRNA to identify structural elements that interact with antibiotic and protein ligands. Using a combination of molecular genetic and biochemical probing techniques, we have concentrated on regions of the rRNA that are connected with specific functions. These are located in different domains within the 23S rRNA and include the ribosomal GTPase-associated center in domain II, which contains the binding sites for r-proteins L10-(L12)4and L11 and is inhibited by interaction with the antibiotic thiostrepton. The peptidyltransferase center within domain V is inhibited by macrolide, lincosamide, and streptogramin B antibiotics, which interact with the rRNA around nucleotide A2058. Drug resistance is conferred by mutations here and by modification of A2058 by ErmE methyltransferase. ErmE recognizes a conserved motif displayed in the primary and secondary structure of the peptidyl transferase loop. Within domain VI of the rRNA, the α-sarcin stem–loop is associated with elongation factor binding and is the target site for ribotoxins including the N-glycosidase ribosome-inactivating proteins ricin and pokeweed antiviral protein (PAP). The orientations of the 23S rRNA domains are constrained by tertiary interactions, including a pseudoknot in domain II and long-range base pairings in the center of the molecule that bring domains II and V closer together. The phenotypic effects of mutations in these regions have been investigated by expressing 23S rRNA from plasmids. Allele-specific priming sites have been introduced close to these structures in the rRNA to enable us to study the molecular events there.Key words: rRNA tertiary structure, rRNA–antibiotic interaction, r-protein binding, Erm methyltransferase, rRNA modification.

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Kim, Ju-Ha, Ji Hoon Jung, Hyo-Jung Lee, Deok-Yong Sim, Eunji Im, Jieon Park, Woon-Yi Park, et al. "UBE2M Drives Hepatocellular Cancer Progression as a p53 Negative Regulator by Binding to MDM2 and Ribosomal Protein L11." Cancers 13, no. 19 (September 29, 2021): 4901. http://dx.doi.org/10.3390/cancers13194901.

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Though UBE2M, an E2 NEDD8-conjugating enzyme, is overexpressed in HepG2, Hep3B, Huh7 and PLC/PRF5 HCCs with poor prognosis by human tissue array and TCGA analysis, its underlying oncogenic mechanism remains unclear. Herein, UBE2M depletion suppressed viability and proliferation and induced cell cycle arrest and apoptosis via cleavages of PARP and caspase 3 and upregulation of p53, Bax and PUMA in HepG2, Huh7 and Hep3B cells. Furthermore, UBE2M depletion activated p53 expression and stability, while the ectopic expression of UBE2M disturbed p53 activation and enhanced degradation of exogenous p53 mediated by MDM2 in HepG2 cells. Interestingly, UBE2M binds to MDM2 or ribosomal protein L11, but not p53 in HepG2 cells, despite crosstalk between p53 and UBE2M. Consistently, the colocalization between UBE2M and MDM2 was observed by immunofluorescence. Notably, L11 was required in p53 activation by UBE2M depletion. Furthermore, UBE2M depletion retarded the growth of HepG2 cells in athymic nude mice along with elevated p53. Overall, these findings suggest that UBE2M promotes cancer progression as a p53 negative regulator by binding to MDM2 and ribosomal protein L11 in HCCs.

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Umaer, Khan, Martin Ciganda, and Noreen Williams. "Ribosome Biogenesis in African Trypanosomes Requires Conserved and Trypanosome-Specific Factors." Eukaryotic Cell 13, no. 6 (April 4, 2014): 727–37. http://dx.doi.org/10.1128/ec.00307-13.

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ABSTRACTLarge ribosomal subunit protein L5 is responsible for the stability and trafficking of 5S rRNA to the site of eukaryotic ribosomal assembly. InTrypanosoma brucei, in addition to L5, trypanosome-specific proteins P34 and P37 also participate in this process. These two essential proteins form a novel preribosomal particle through interactions with both the ribosomal protein L5 and 5S rRNA. We have generated a procyclic L5 RNA interference cell line and found that L5 itself is a protein essential for trypanosome growth, despite the presence of other 5S rRNA binding proteins. Loss of L5 decreases the levels of all large-subunit rRNAs, 25/28S, 5.8S, and 5S rRNAs, but does not alter small-subunit 18S rRNA. Depletion of L5 specifically reduced the levels of the other large ribosomal proteins, L3 and L11, whereas the steady-state levels of the mRNA for these proteins were increased. L5-knockdown cells showed an increase in the 40S ribosomal subunit and a loss of the 60S ribosomal subunits, 80S monosomes, and polysomes. In addition, L5 was involved in the processing and maturation of precursor rRNAs. Analysis of polysomal fractions revealed that unprocessed rRNA intermediates accumulate in the ribosome when L5 is depleted. Although we previously found that the loss of P34 and P37 does not result in a change in the levels of L5, the loss of L5 resulted in an increase of P34 and P37 proteins, suggesting the presence of a compensatory feedback loop. This study demonstrates that ribosomal protein L5 has conserved functions, in addition to nonconserved trypanosome-specific features, which could be targeted for drug intervention.

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29

Demirci, H., S. T. Gregory, A. E. Dahlberg, and G. Jogl. "Recognition and catalysis of ribosomal protein L11 by the protein trimethyltransferase PrmA." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C374. http://dx.doi.org/10.1107/s0108767308088065.

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30

Gazda, Hanna T., Mee Rie Sheen, Natasha Darras, Hal Shneider, Colin A. Sieff, Sarah E. Ball, Edyta Niewiadomska, et al. "Mutations of the Genes for Ribosomal Proteins L5 and L11 Are a Common Cause of Diamond-Blackfan Anemia." Blood 110, no. 11 (November 16, 2007): 421. http://dx.doi.org/10.1182/blood.v110.11.421.421.

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Abstract Diamond-Blackfan anemia (DBA), a form of congenital red cell aplasia with marked clinical heterogeneity and increased risk of malignancy, has been associated with mutations in ribosomal protein (RP) gene RPS19 in 25% of probands and in RPS24 or RPS17 in ∼2% of patients. Thus, DBA appears to be a disorder of ribosome synthesis. To test the hypothesis that mutations in other RP genes may also cause DBA, we carried out direct sequencing of candidate RP genes. Genomic DNA samples from 96 unrelated DBA probands (14 familial and 82 sporadic cases) without RPS19 or RPS24 mutations were screened for mutations in RPS3a, RPS13, and RPS16 (previous studies revealed that RPs S19, S24, S3a, S13, and S16 are involved in binding of eIF-2 to the 40S subunit); RP genes L18, L13A, L36, L28, L18A, L40, S5, S9, S11, and S28 (located on chromosome 19); and RP genes, L5, L11, L22, S8, and S27 (on chromosome 1). PCR primers were designed to amplify the coding exons and intron/exon boundaries. We found multiple mutations in two RP genes, L5 and L11. Subsequently we sequenced these two genes in 42 additional DNA samples from DBA probands. In total, we screened 5′UTR, promoter and coding regions, and exon/intron boundaries of RPL5 and RPL11 in 138 DBA unrelated probands. We identified 14 mutations in RPL5 in 138 probands (∼10%), 13 of which are nonsense mutations, deletions or insertions of 1–5 nucleotides causing frameshift and premature termination. One missense mutation, 418G>A, results in a G140S substitution. We found nine mutations in RPL11 in138 DBA probands (6.5%), including five acceptor or donor splice site mutations (introns 1–4) and four deletions or insertions of 1–4 nucleotides causing frameshifts (codons 32-120). None of these sequence changes were found on the NCBI (http://www.ncbi.nlm.nih.gov/SNP/) or the HapMap (http://www.hapmap.org/) SNP lists. Both genes, as well as RPL23 have recently been demonstrated by others to activate the p53 tumor suppressor protein by inhibiting MDM2-mediated p53 ubiquitination and degradation. Moreover, knockdown of any of these genes by siRNAs markedly reduced p53 induction by the ribosomal biogenesis stressor, actinomycin-D. These findings suggest that DBA patients with mutated L5 and L11 proteins may have inadequate p53 pathway activation and (consistent with clinical observations) be at increased risk for neoplasia. We are currently investigating the role of RPL5 and RPL11 mutations in ribosomal biogenesis and in the p53-mediated cell cycle arrest and apoptosis in DBA patients.

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31

Vanet, Anne, Jacqueline A. Plumbridge, Marie-France Guérin, and Jean-Hervé Alix. "Ribosomal protein methylation in Escherichia coli: the gene prmA, encoding the ribosomal protein L11 methyltransferase, is dispensable." Molecular Microbiology 14, no. 5 (December 1994): 947–58. http://dx.doi.org/10.1111/j.1365-2958.1994.tb01330.x.

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32

Shimmin, L. C., and P. P. Dennis. "Characterization of the L11, L1, L10 and L12 equivalent ribosomal protein gene cluster of the halophilic archaebacterium Halobacterium cutirubrum." EMBO Journal 8, no. 4 (April 1989): 1225–35. http://dx.doi.org/10.1002/j.1460-2075.1989.tb03496.x.

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33

Demirci, Hasan, Steven T. Gregory, Albert E. Dahlberg, and Gerwald Jogl. "Multiple-Site Trimethylation of Ribosomal Protein L11 by the PrmA Methyltransferase." Structure 16, no. 7 (July 2008): 1059–66. http://dx.doi.org/10.1016/j.str.2008.03.016.

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34

Van Dyke, Natalya, Wenbing Xu, and Emanuel J. Murgola. "Limitation of Ribosomal Protein L11 Availability in vivo Affects Translation Termination." Journal of Molecular Biology 319, no. 2 (May 2002): 329–39. http://dx.doi.org/10.1016/s0022-2836(02)00304-2.

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35

Jung, Ji Hoon, Hyo-Jung Lee, Ju-Ha Kim, Deok Yong Sim, Eunji Im, Sinae Kim, Suhwan Chang, and Sung-Hoon Kim. "Colocalization of MID1IP1 and c-Myc is Critically Involved in Liver Cancer Growth via Regulation of Ribosomal Protein L5 and L11 and CNOT2." Cells 9, no. 4 (April 16, 2020): 985. http://dx.doi.org/10.3390/cells9040985.

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Though midline1 interacting protein 1 (MID1IP1) was known as one of the glucose-responsive genes regulated by carbohydrate response element binding protein (ChREBP), the underlying mechanisms for its oncogenic role were never explored. Thus, in the present study, the underlying molecular mechanism of MID1P1 was elucidated mainly in HepG2 and Huh7 hepatocellular carcinoma cells (HCCs). MID1IP1 was highly expressed in HepG2, Huh7, SK-Hep1, PLC/PRF5, and immortalized hepatocyte LX-2 cells more than in normal hepatocyte AML-12 cells. MID1IP1 depletion reduced the viability and the number of colonies and also increased sub G1 population and the number of TUNEL-positive cells in HepG2 and Huh7 cells. Consistently, MID1IP1 depletion attenuated pro-poly (ADP-ribose) polymerase (pro-PARP), c-Myc and activated p21, while MID1IP1 overexpression activated c-Myc and reduced p21. Furthermore, MID1IP1 depletion synergistically attenuated c-Myc stability in HepG2 and Huh7 cells. Of note, MID1IP1 depletion upregulated the expression of ribosomal protein L5 or L11, while loss of L5 or L11 rescued c-Myc in MID1IP1 depleted HepG2 and Huh7 cells. Interestingly, tissue array showed that the overexpression of MID1IP1 was colocalized with c-Myc in human HCC tissues, which was verified in HepG2 and Huh7 cells by Immunofluorescence. Notably, depletion of CCR4-NOT2 (CNOT2) with adipogenic activity enhanced the antitumor effect of MID1IP1 depletion to reduce c-Myc, procaspase 3 and pro-PARP in HepG2, Huh7 and HCT116 cells. Overall, these findings provide novel insight that MID1IP1 promotes the growth of liver cancer via colocalization with c-Myc mediated by ribosomal proteins L5 and L11 and CNOT2 as a potent oncogenic molecule.

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36

Asano, Nozomi, Akiyoshi Nakamura, Keisuke Komoda, Koji Kato, Isao Tanaka, and Min Yao. "Crystallization and preliminary X-ray crystallographic analysis of ribosome assembly factors: the Rpf2–Rrs1 complex." Acta Crystallographica Section F Structural Biology Communications 70, no. 12 (November 14, 2014): 1649–52. http://dx.doi.org/10.1107/s2053230x14024182.

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Rpf2 and Rrs1 are essential proteins for ribosome biogenesis. These proteins form a complex (the Rpf2-subcomplex) with 5S rRNA and two ribosomal proteins (L5 and L11). This complex is recruited to the ribosome precursor (the 90S pre-ribosome). This recruitment is necessary for the maturation of 25S rRNA. Genetic depletion of Rpf2 and Rrs1 results in accumulation of the 25S rRNA precursor. In this study, Rpf2 and Rrs1 fromAspergillus nidulanswere co-overexpressed inEscherichia coli, purified and crystallized. Subsequent analysis revealed that these crystals contained the central core region of the complex consisting of both N-terminal domains. X-ray diffraction data were collected to 2.35 Å resolution. Preliminary analysis revealed that the crystals belonged to space groupP212121, with unit-cell parametersa= 54.1,b= 123.3,c = 133.8 Å. There are two complexes in the asymmetric unit. Structure determination using selenomethionine-labelled protein is in progress.

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37

Ramirez, Celia, Lawrence C. Shimmin, Peter Leggatt, and Alastair T. Matheson. "Structure and Transcription of the L11-L1-L10-L12 Ribosomal Protein Gene Operon from the Extreme Thermophilic Archaeon Sulfolobus acidocaldarius." Journal of Molecular Biology 244, no. 2 (November 1994): 242–49. http://dx.doi.org/10.1006/jmbi.1994.1723.

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38

Sun, Xiao-Xin, Yue-Gang Wang, Dimitris P. Xirodimas, and Mu-Shui Dai. "Perturbation of 60 S Ribosomal Biogenesis Results in Ribosomal Protein L5- and L11-dependent p53 Activation." Journal of Biological Chemistry 285, no. 33 (June 16, 2010): 25812–21. http://dx.doi.org/10.1074/jbc.m109.098442.

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39

Todorova, Roumiana. "Cloning, purification and characterization of the ribosomal protein L11 from E. coli." American Journal of Molecular Biology 01, no. 01 (2011): 33–42. http://dx.doi.org/10.4236/ajmb.2011.11005.

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40

Danilova, Nadia, Kathleen M. Sakamoto, and Shuo Lin. "Ribosomal protein L11 mutation in zebrafish leads to haematopoietic and metabolic defects." British Journal of Haematology 152, no. 2 (November 29, 2010): 217–28. http://dx.doi.org/10.1111/j.1365-2141.2010.08396.x.

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41

Heinrich, Tatjana, Volker A. Erdmann, and Roland K. Hartmann. "Sequence of the gene encoding ribosomal protein L11 from Thermus thermophilus HB8." Gene 136, no. 1-2 (December 1993): 373–74. http://dx.doi.org/10.1016/0378-1119(93)90500-3.

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42

Ochi, K., D. Zhang, S. Kawamoto, and A. Hesketh. "Molecular and functional analysis of the ribosomal L11 and S12 protein genes (." MGG - Molecular & General Genetics 256, no. 5 (1997): 488. http://dx.doi.org/10.1007/s004380050593.

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43

Miyoshi, Keita, Chiharu Shirai, Chihiro Horigome, Kazuhiko Takenami, Junko Kawasaki, and Keiko Mizuta. "Rrs1p, a ribosomal protein L11-binding protein, is required for nuclear export of the 60S pre-ribosomal subunit inSaccharomyces cerevisiae." FEBS Letters 565, no. 1-3 (April 9, 2004): 106–10. http://dx.doi.org/10.1016/j.febslet.2004.03.087.

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44

Challagundla, K. B., X. X. Sun, X. Zhang, T. DeVine, Q. Zhang, R. C. Sears, and M. S. Dai. "Ribosomal Protein L11 Recruits miR-24/miRISC To Repress c-Myc Expression in Response to Ribosomal Stress." Molecular and Cellular Biology 31, no. 19 (August 1, 2011): 4007–21. http://dx.doi.org/10.1128/mcb.05810-11.

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45

Dai, Mu-Shui, Xiao-Xin Sun, and Hua Lu. "Aberrant Expression of Nucleostemin Activates p53 and Induces Cell Cycle Arrest via Inhibition of MDM2." Molecular and Cellular Biology 28, no. 13 (April 21, 2008): 4365–76. http://dx.doi.org/10.1128/mcb.01662-07.

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ABSTRACT The nucleolar protein nucleostemin (NS) is essential for cell proliferation and early embryogenesis. Both depletion and overexpression of NS reduce cell proliferation. However, the mechanisms underlying this regulation are still unclear. Here, we show that NS regulates p53 activity through the inhibition of MDM2. NS binds to the central acidic domain of MDM2 and inhibits MDM2-mediated p53 ubiquitylation and degradation. Consequently, ectopic overexpression of NS activates p53, induces G1 cell cycle arrest, and inhibits cell proliferation. Interestingly, the knockdown of NS by small interfering RNA also activates p53 and induces G1 arrest. These effects require the ribosomal proteins L5 and L11, since the depletion of NS enhanced their interactions with MDM2 and the knockdown of L5 or L11 abrogated the NS depletion-induced p53 activation and cell cycle arrest. These results suggest that a p53-dependent cell cycle checkpoint monitors changes of cellular NS levels via the impediment of MDM2 function.

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46

Dai, Mu-Shui, Kishore B. Challagundla, Xiao-Xin Sun, Lakshmi Reddy Palam, Shelya X. Zeng, Ronald C. Wek, and Hua Lu. "Physical and Functional Interaction between Ribosomal Protein L11 and the Tumor Suppressor ARF." Journal of Biological Chemistry 287, no. 21 (March 30, 2012): 17120–29. http://dx.doi.org/10.1074/jbc.m111.311902.

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47

Rhodin, Michael H. J., and Jonathan D. Dinman. "A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding." Nucleic Acids Research 38, no. 22 (August 12, 2010): 8377–89. http://dx.doi.org/10.1093/nar/gkq711.

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48

Xing, Yanyan, Debraj GuhaThakurta, and David E. Draper. "The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains." Nature Structural & Molecular Biology 4, no. 1 (January 1997): 24–27. http://dx.doi.org/10.1038/nsb0197-24.

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49

Bhat, Krishna P., Koji Itahana, Aiwen Jin, and Yanping Zhang. "Essential role of ribosomal protein L11 in mediating growth inhibition-induced p53 activation." EMBO Journal 23, no. 12 (May 20, 2004): 2402–12. http://dx.doi.org/10.1038/sj.emboj.7600247.

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50

Larochelle, Stephane, and Beat Suter. "Molecular cloning of the Drosophila homologue of the rat ribosomal protein L11 gene." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1261, no. 1 (March 1995): 147–50. http://dx.doi.org/10.1016/0167-4781(95)00010-e.

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