scholarly journals Nascent alt-protein chemoproteomics reveals a repressor of ribosome biogenesis

2021 ◽  
Author(s):  
Sarah Slavoff ◽  
Xiongwen Cao ◽  
Alexandra Khitun ◽  
Cecelia Harold ◽  
Carson Bryant ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Dna Damage ◽  
Protein Synthesis ◽  
Late Stage ◽  
Ribosome Biogenesis ◽  
Ribosomal Subunit ◽  
Human Cells ◽  
Subunit A ◽  
Global Protein Synthesis

Abstract Many unannotated microproteins and alternative proteins (alt-proteins) have recently been found to be co-encoded with canonical proteins, but few of their functions are known. Motivated by the hypothesis that alt-proteins undergoing active or stress-induced synthesis could play important cellular roles, here, we developed a chemoproteomic pipeline to identify nascent alt-proteins in human cells. We identified 22 actively translated unannotated alt-proteins, one of which is upregulated after DNA damage stress. We further defined MINAS-60 (MIcroprotein that Negatively regulates ASsembly of the pre-60S ribosomal subunit), a nucleolar localized alt-protein co-encoded with human RBM10. Depletion of MINAS-60 increases the amount of the mature 60S ribosomal subunit, consequently upregulating global protein synthesis and cell proliferation by repressing late-stage pre-60S assembly and export of the 60S ribosome subunit to the cytoplasm. Together, these results implicate MINAS-60 as a repressor of ribosome biogenesis, and demonstrate that chemoproteomics can enable generation of functional hypotheses for uncharacterized alt-proteins.

scholarly journals The human RBM10 gene dually encodes a repressor of ribosome biogenesis that downregulates cell proliferation

2021 ◽  
Author(s):  
xiongwen cao ◽  
Cecelia M. Harold ◽  
Carson J. Bryant ◽  
Shu-Jian Zheng ◽  
Alexandra Khitun ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Global Protein Synthesis ◽  
Acid Protein ◽  
Splicing Regulator ◽  
Inhibit Cell Proliferation ◽  
Amino Acid Protein

Ribosome biogenesis in eukaryotes is a highly regulated, essential cellular process. However, few repressors of ribosome biogenesis have been identified. Here, we identify and define the function of MINAS-60 (MIcroprotein that Negatively regulates ASsembly of the pre-60S ribosomal subunit), a 130-amino acid protein co-encoded with the human pre-mRNA splicing regulator and tumor suppressor protein RBM10. MINAS-60 localizes to the nucleolus, where it associates with multiple pre-60S assembly factors. Depletion of MINAS-60 increases the amount of mature 60S ribosomal subunit in the cytoplasm and, consequently, upregulates global protein synthesis and cell proliferation. Mechanistically, we show that MINAS-60 represses late-stage pre-60S assembly and export of the mature 60S ribosome subunit to the cytoplasm. Together, these results implicate MINAS-60 as a repressor of ribosome biogenesis that acts as a checkpoint for the maturation of the large subunit (LSU). More broadly, the RBM10 transcript encodes two sequence-independent proteins that inhibit cell proliferation via different molecular mechanisms, expanding existing models of multicistronic human gene functions.

scholarly journals Las1L Is a Nucleolar Protein Required for Cell Proliferation and Ribosome Biogenesis

2010 ◽  
Vol 30 (18) ◽  
pp. 4404-4414 ◽  
Author(s):  
Christopher D. Castle ◽  
Erica K. Cassimere ◽  
Jinho Lee ◽  
Catherine Denicourt
Keyword(s):  
Cell Proliferation ◽  
Cell Growth ◽  
Ribosome Biogenesis ◽  
Ribosomal Subunit ◽  
Nucleolar Protein ◽  
28S Rrna ◽  
Rrna Processing ◽  
Tumor Suppressor P53 ◽  
Growth Increase ◽  
Multistep Process

ABSTRACT Ribosome biogenesis is a highly regulated process ensuring that cell growth (increase in biomass) is coordinated with cell proliferation. The formation of eukaryotic ribosomes is a multistep process initiated by the transcription and processing of rRNA in the nucleolus. Concomitant with this, several preribosomal particles, which transiently associate with numerous nonribosomal factors before mature 60S and 40S subunits are formed and exported in the cytoplasm, are generated. Here we identify Las1L as a previously uncharacterized nucleolar protein required for ribosome biogenesis. Depletion of Las1L causes inhibition of cell proliferation characterized by a G1 arrest dependent on the tumor suppressor p53. Moreover, we demonstrate that Las1L is crucial for ribosome biogenesis and that depletion of Las1L leads to inhibition of rRNA processing and failure to synthesize the mature 28S rRNA. Taken together, our data demonstrate that Las1L is essential for cell proliferation and biogenesis of the 60S ribosomal subunit.

scholarly journals Solithromycin Inhibition of Protein Synthesis and Ribosome Biogenesis in Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae

2013 ◽  
Vol 57 (4) ◽  
pp. 1632-1637 ◽  
Author(s):  
Ward Rodgers ◽  
Ashley D. Frazier ◽  
W. Scott Champney
Keyword(s):  
Staphylococcus Aureus ◽  
Protein Synthesis ◽  
Streptococcus Pneumoniae ◽  
Haemophilus Influenzae ◽  
Ribosome Biogenesis ◽  
Antimicrobial Agents ◽  
Protein Biosynthesis ◽  
Ribosomal Subunit ◽  
23S Rrna ◽  
Content Type

ABSTRACTThe continuing increase in antibiotic-resistant microorganisms is driving the search for new antibiotic targets and improved antimicrobial agents. Ketolides are semisynthetic derivatives of macrolide antibiotics, which are effective against certain resistant organisms. Solithromycin (CEM-101) is a novel fluoroketolide with improved antimicrobial effectiveness. This compound binds to the large 50S subunit of the ribosome and inhibits protein biosynthesis. Like other ketolides, it should impair bacterial ribosomal subunit formation. This mechanism of action was examined in strains ofStreptococcus pneumoniae,Staphylococcus aureus, andHaemophilus influenzae. The mean 50% inhibitory concentrations (IC50s) for solithromycin inhibition of cell viability, protein synthesis, and growth rate were 7.5, 40, and 125 ng/ml forStreptococcus pneumoniae,Staphylococcus aureus, andHaemophilus influenzae, respectively. The net formation of the 50S subunit was reduced in all three organisms, with IC50s similar to those given above. The rates of 50S subunit formation measured by a pulse-chase labeling procedure were reduced by 75% in cells growing at the IC50of solithromycin. Turnover of 23S rRNA was stimulated by solithromycin as well. Solithromycin was found to be a particularly effective antimicrobial agent, with IC50s comparable to those of telithromycin and significantly better than those of azithromycin and clarithromycin in these three microorganisms.

scholarly journals Translation Stress Regulates Ribosome Synthesis and Cell Proliferation

2018 ◽  
Vol 19 (12) ◽  
pp. 3757 ◽  
Author(s):  
Sivakumar Vadivel Gnanasundram ◽  
Robin Fåhraeus
Keyword(s):  
Protein Synthesis ◽  
Ribosome Biogenesis ◽  
Developmental Disorders ◽  
Mrna Translation ◽  
Cellular Growth ◽  
Pol I ◽  
Global Protein Synthesis ◽  
Sense And Respond ◽  
Pol Iii ◽  
Factor C

Ribosome and protein synthesis are major metabolic events that control cellular growth and proliferation. Impairment in ribosome biogenesis pathways and mRNA translation is associated with pathologies such as cancer and developmental disorders. Processes that control global protein synthesis are tightly regulated at different levels by numerous factors and linked with multiple cellular signaling pathways. Several of these merge on the growth promoting factor c-Myc, which induces ribosome biogenesis by stimulating Pol I, Pol II, and Pol III transcription. However, how cells sense and respond to mRNA translation stress is not well understood. It was more recently shown that mRNA translation stress activates c-Myc, through a specific induction of E2F1 synthesis via a PI3Kδ-dependent pathway. This review focuses on how this novel feedback pathway stimulates cellular growth and proliferation pathways to synchronize protein synthesis with ribosome biogenesis. It also describes for the first time the oncogenic activity of the mRNA, and not the encoded protein.

scholarly journals TOP mRNPs: Molecular Mechanisms and Principles of Regulation

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 969 ◽  
Author(s):  
Eric Cockman ◽  
Paul Anderson ◽  
Pavel Ivanov
Keyword(s):  
Protein Synthesis ◽  
Translational Control ◽  
Gene Networks ◽  
Cellular Response ◽  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Mrna Translation ◽  
Ribonucleoprotein Complexes ◽  
Global Protein Synthesis ◽  
Protein Components

The cellular response to changes in the surrounding environment and to stress requires the coregulation of gene networks aiming to conserve energy and resources. This is often achieved by downregulating protein synthesis. The 5’ Terminal OligoPyrimidine (5’ TOP) motif-containing mRNAs, which encode proteins that are essential for protein synthesis, are the primary targets of translational control under stress. The TOP motif is a cis-regulatory RNA element that begins directly after the m7G cap structure and contains the hallmark invariant 5’-cytidine followed by an uninterrupted tract of 4–15 pyrimidines. Regulation of translation via the TOP motif coordinates global protein synthesis with simultaneous co-expression of the protein components required for ribosome biogenesis. In this review, we discuss architecture of TOP mRNA-containing ribonucleoprotein complexes, the principles of their assembly, and the modes of regulation of TOP mRNA translation.

scholarly journals Amyloid Precursor Protein (APP) Affects Global Protein Synthesis in Dividing Human Cells

2015 ◽  
Vol 230 (5) ◽  
pp. 1064-1074 ◽  
Author(s):  
Anna Sobol ◽  
Paola Galluzzo ◽  
Shuang Liang ◽  
Brittany Rambo ◽  
Sylvia Skucha ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Amyloid Precursor Protein ◽  
Human Cells ◽  
Precursor Protein ◽  
Global Protein Synthesis

scholarly journals RNAmetasome network for macromolecule biogenesis in human cells

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shiro Iuchi ◽  
Joao A. Paulo
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cell Proliferation ◽  
Chromatin Remodeling ◽  
Ribosome Biogenesis ◽  
Human Cells ◽  
The Other ◽  
Core Proteins ◽  
Functional Forms ◽  
Low Expression

AbstractRNA plays a central role in macromolecule biogenesis for various pathways, such as gene expression, ribosome biogenesis, and chromatin remodeling. However, RNA must be converted from its nascent to functional forms for that role. Here, we describe a large RNA metabolic network (RNAmetasome network) for macromolecule biogenesis in human cells. In HEK293T, the network consists of proteins responsible for gene expression, splicing, ribosome biogenesis, chromatin remodeling, and cell cycle. Reciprocal immunoprecipitations show that MKI67, GNL2, MDN1, and ELMSAN1 are core proteins of the network, and knockdown of either MKI67 or GNL2 affects the state of the other protein, MDN1, and some other network members. Furthermore, GNL2 knockdown retards cell proliferation. Several proteins of the RNAmetasome network are diminished in Hela.cl1, and this diminishment is associated with low expression of MDN1 and elevated MKI67 degradation. These results together suggest that the RNAmetasome network is present in human cells and associated with proliferation, and that MKI67, GNL2, and MDN1 play an important role in organizing the RNAmetasome network.

scholarly journals Hygromycin B Inhibition of Protein Synthesis and Ribosome Biogenesis in Escherichia coli

2006 ◽  
Vol 51 (2) ◽  
pp. 591-596 ◽  
Author(s):  
Susan M. McGaha ◽  
W. Scott Champney
Keyword(s):  
Escherichia Coli ◽  
Protein Synthesis ◽  
16S Rrna ◽  
Ribosome Biogenesis ◽  
Ribosomal Subunit ◽  
Aminoglycoside Antibiotic ◽  
Viable Cell ◽  
Northern Hybridization ◽  
Hygromycin B ◽  
E Coli

ABSTRACT The aminoglycoside antibiotic hygromycin B was examined in Escherichia coli cells for inhibitory effects on translation and ribosomal-subunit formation. Pulse-chase labeling experiments were performed, which verified lower rates of ribosomal-subunit synthesis in drug-treated cells. Hygromycin B exhibited a concentration-dependent inhibitory effect on viable-cell numbers, growth rate, protein synthesis, and 30S and 50S subunit formation. Unlike other aminoglycosides, hygromycin B was a more effective inhibitor of translation than of ribosomal-subunit formation in E. coli. Examination of total RNA from treated cells showed an increase in RNA corresponding to a precursor to the 16S rRNA, while mature 16S rRNA decreased. Northern hybridization to rRNA in cells treated with hygromycin B showed that RNase II- and RNase III-deficient strains of E. coli accumulated 16S rRNA fragments upon treatment with the drug. The results indicate that hygromycin B targets protein synthesis and 30S ribosomal-subunit assembly.

scholarly journals RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit

2020 ◽  
Author(s):  
Emilie L. Cerezo ◽  
Thibault Houles ◽  
Oriane Lié ◽  
Marie-Kerguelen Sarthou ◽  
Charlotte Audoynaud ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Ribosome Biogenesis ◽  
Mapk Pathway ◽  
Ribosomal Subunit ◽  
Mitogen Activated Protein Kinase ◽  
Particle Assembly ◽  
Ribosomal Subunits ◽  
Mitogen Activated Protein ◽  
Assembly Factor ◽  
Cell Growth And Proliferation

AbstractRibosome biogenesis lies at the nexus of various signaling pathways coordinating protein synthesis with cell growth and proliferation. This process is regulated by well-described transcriptional mechanisms, but a growing body of evidence indicates that other levels of regulation exist. Here we show that the Ras/mitogen-activated protein kinase (MAPK) pathway stimulates post-transcriptional stages of human ribosome synthesis. We identify RIOK2, a pre-40S particle assembly factor, as a new target of the MAPK-activated kinase RSK. RIOK2 phosphorylation by RSK promotes cytoplasmic maturation of late pre-40S particles, which is required for optimal protein synthesis and cell proliferation. RIOK2 phosphorylation facilitates its release from pre-40S particles and its nuclear re-import, prior to completion of small ribosomal subunits. Our results bring a detailed mechanistic link between the Ras/MAPK pathway and the maturation of human pre-40S particles, which open a hitherto poorly explored area of ribosome biogenesis.

scholarly journals The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis

2015 ◽  
Vol 26 (11) ◽  
pp. 2080-2095 ◽  
Author(s):  
Christiane Zorbas ◽  
Emilien Nicolas ◽  
Ludivine Wacheul ◽  
Emmeline Huvelle ◽  
Valérie Heurgué-Hamard ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
18S Rrna ◽  
Control Mechanism ◽  
Budding Yeast ◽  
Ribosomal Subunit ◽  
Human Cells ◽  
Rrna Processing ◽  
Distinctive Features ◽  
Catalytic Function ◽  
Quality Control Mechanism

At the heart of the ribosome lie rRNAs, whose catalytic function in translation is subtly modulated by posttranscriptional modifications. In the small ribosomal subunit of budding yeast, on the 18S rRNA, two adjacent adenosines (A1781/A1782) are N6-dimethylated by Dim1 near the decoding site, and one guanosine (G1575) is N7-methylated by Bud23-Trm112 at a ridge between the P- and E-site tRNAs. Here we establish human DIMT1L and WBSCR22-TRMT112 as the functional homologues of yeast Dim1 and Bud23-Trm112. We report that these enzymes are required for distinct pre-rRNA processing reactions leading to synthesis of 18S rRNA, and we demonstrate that in human cells, as in budding yeast, ribosome biogenesis requires the presence of the modification enzyme rather than its RNA-modifying catalytic activity. We conclude that a quality control mechanism has been conserved from yeast to human by which binding of a methyltransferase to nascent pre-rRNAs is a prerequisite to processing, so that all cleaved RNAs are committed to faithful modification. We further report that 18S rRNA dimethylation is nuclear in human cells, in contrast to yeast, where it is cytoplasmic. Yeast and human ribosome biogenesis thus have both conserved and distinctive features.

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