scholarly journals How Many Messenger RNAs Can Be Translated by the START Mechanism?

2020 ◽  
Vol 21 (21) ◽  
pp. 8373
Author(s):  
Laurence Despons ◽  
Franck Martin
Keyword(s):  
Messenger Rna ◽  
Mrna Translation ◽  
Start Codon ◽  
Messenger Rnas ◽  
Coding Sequences ◽  
Coding Sequence ◽  
Rna Translation ◽  
Codon Recognition ◽  
G Quadruplex ◽  
Stable Structures

Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. “Structure Assisted RNA Translation”, or “START”, has been proposed to use stable secondary structures located in the coding sequence to augment start site selection by steric hindrance of the progression of pre-initiation complex on messenger RNA. This implies that such structures have to be located downstream and at on optimal distance from the AUG start codon (i.e., downstream nucleotide +16). In order to assess the importance of the START mechanism in the overall mRNA translation process, we developed a bioinformatic tool to screen coding sequences for such stable structures in a 50 nucleotide-long window spanning the nucleotides from +16 to +65. We screened eight bacterial genomes and six eukaryotic genomes. We found stable structures in 0.6–2.5% of eukaryotic coding sequences. Among these, approximately half of them were structures predicted to form G-quadruplex structures. In humans, we selected 747 structures. In bacteria, the coding sequences from Gram-positive bacteria contained 2.6–4.2% stable structures, whereas the structures were less abundant in Gram-negative bacteria (0.2–2.7%). In contrast to eukaryotes, putative G-quadruplex structures are very rare in the coding sequence of bacteria. Altogether, our study reveals that the START mechanism seems to be an ancient strategy to facilitate the start codon recognition that is used in different kingdoms of life.

scholarly journals The different activities of RNA G-quadruplex structures are controlled by flanking sequences

2021 ◽  
Vol 5 (2) ◽  
pp. e202101232
Author(s):  
Alice J-L Zheng ◽  
Aikaterini Thermou ◽  
Pedro Guixens Gallardo ◽  
Laurence Malbert-Colas ◽  
Chrysoula Daskalogianni ◽  
...  
Keyword(s):  
Immune Evasion ◽  
Mrna Translation ◽  
Repeat Sequence ◽  
Rna Structures ◽  
Coding Sequences ◽  
Translation Inhibition ◽  
G Quadruplex ◽  
Flanking Sequences ◽  
Context Dependent

The role of G-quadruplex (G4) RNA structures is multifaceted and controversial. Here, we have used as a model the EBV-encoded EBNA1 and the Kaposi’s sarcoma-associated herpesvirus (KSHV)-encoded LANA1 mRNAs. We have compared the G4s in these two messages in terms of nucleolin binding, nuclear mRNA retention, and mRNA translation inhibition and their effects on immune evasion. The G4s in the EBNA1 message are clustered in one repeat sequence and the G4 ligand PhenDH2 prevents all G4-associated activities. The RNA G4s in the LANA1 message take part in similar multiple mRNA functions but are spread throughout the message. The different G4 activities depend on flanking coding and non-coding sequences and, interestingly, can be separated individually. Together, the results illustrate the multifunctional, dynamic and context-dependent nature of G4 RNAs and highlight the possibility to develop ligands targeting specific RNA G4 functions. The data also suggest a common multifunctional repertoire of viral G4 RNA activities for immune evasion.

Translational pathophysiology: a novel molecular mechanism of human disease

Blood ◽  
2000 ◽  
Vol 95 (11) ◽  
pp. 3280-3288 ◽  
Author(s):  
Mario Cazzola ◽  
Radek C. Skoda
Keyword(s):  
Human Disease ◽  
Messenger Rna ◽  
Rna Binding ◽  
Kinase Inhibitor ◽  
Rna Binding Proteins ◽  
Point Mutations ◽  
Ribosomal Subunit ◽  
Mrna Translation ◽  
Start Codon ◽  
Stem Loop

Abstract In higher eukaryotes, the expression of about 1 gene in 10 is strongly regulated at the level of messenger RNA (mRNA) translation into protein. Negative regulatory effects are often mediated by the 5′-untranslated region (5′-UTR) and rely on the fact that the 40S ribosomal subunit first binds to the cap structure at the 5′-end of mRNA and then scans for the first AUG codon. Self-complementary sequences can form stable stem-loop structures that interfere with the assembly of the preinitiation complex and/or ribosomal scanning. These stem loops can be further stabilized by the interaction with RNA-binding proteins, as in the case of ferritin. The presence of AUG codons located upstream of the physiological start site can inhibit translation by causing premature initiation and thereby preventing the ribosome from reaching the physiological start codon, as in the case of thrombopoietin (TPO). Recently, mutations that cause disease through increased or decreased efficiency of mRNA translation have been discovered, defining translational pathophysiology as a novel mechanism of human disease. Hereditary hyperferritinemia/cataract syndrome arises from various point mutations or deletions within a protein-binding sequence in the 5′-UTR of the L-ferritin mRNA. Each unique mutation confers a characteristic degree of hyperferritinemia and severity of cataract in affected individuals. Hereditary thrombocythemia (sometimes called familial essential thrombocythemia or familial thrombocytosis) can be caused by mutations in upstream AUG codons in the 5′-UTR of the TPO mRNA that normally function as translational repressors. Their inactivation leads to excessive production of TPO and elevated platelet counts. Finally, predisposition to melanoma may originate from mutations that create translational repressors in the 5′-UTR of the cyclin-dependent kinase inhibitor–2A gene.

scholarly journals Translation Initiation Factor 2γ Mutant Alters Start Codon Selection Independent of Met-tRNA Binding

2008 ◽  
Vol 28 (22) ◽  
pp. 6877-6888 ◽  
Author(s):  
Pankaj V. Alone ◽  
Chune Cao ◽  
Thomas E. Dever
Keyword(s):  
Binding Affinity ◽  
Translation Initiation ◽  
Ribosomal Subunit ◽  
Mrna Translation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Start Codon ◽  
Codon Recognition ◽  
40S Ribosomal Subunit ◽  
Initiation Factor 2

ABSTRACT Selection of the AUG start codon for translation in eukaryotes is governed by codon-anticodon interactions between the initiator Met-tRNAi Met and the mRNA. Translation initiation factor 2 (eIF2) binds Met-tRNAi Met to the 40S ribosomal subunit, and previous studies identified Sui− mutations in eIF2 that enhanced initiation from a noncanonical UUG codon, presumably by impairing Met-tRNAi Met binding. Consistently, an eIF2γ-N135D GTP-binding domain mutation impairs Met-tRNAi Met binding and causes a Sui− phenotype. Intragenic A208V and A382V suppressor mutations restore Met-tRNAi Met binding affinity and cell growth; however, only A208V suppresses the Sui− phenotype associated with the eIF2γ-N135D mutation. An eIF2γ-A219T mutation impairs Met-tRNAi Met binding but unexpectedly enhances the fidelity of initiation, suppressing the Sui− phenotype associated with the eIF2γ-N135D,A382V mutant. Overexpression of eIF1, which is thought to monitor codon-anticodon interactions during translation initiation, likewise suppresses the Sui− phenotype of the eIF2γ mutants. We propose that structural alterations in eIF2γ subtly alter the conformation of Met-tRNAi Met on the 40S subunit and thereby affect the fidelity of start codon recognition independent of Met-tRNAi Met binding affinity.

scholarly journals Large ribosomal subunit, eIF5B, Met-tRNAiMet and mRNA cooperate to complete accurate initiation

2020 ◽  
Author(s):  
Jinfan Wang ◽  
Jing Wang ◽  
Byung-Sik Shin ◽  
Thomas E. Dever ◽  
Joseph D. Puglisi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Translation Initiation ◽  
Messenger Rna ◽  
Ribosomal Subunit ◽  
Mrna Translation ◽  
Start Codon ◽  
Large Ribosomal Subunit ◽  
Gtp Hydrolysis ◽  
Reading Frame ◽  
Fluorescence Measurements

AbstractRecognition of a start codon by the first aminoacyl-tRNA (Met-tRNAiMet) determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determined the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovered an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.One sentence summaryCryoEM structure of a naturally long-lived translation initiation intermediate with Met-tRNAiMet and eIF5B post GTP hydrolysis.

scholarly journals Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jinfan Wang ◽  
Jing Wang ◽  
Byung-Sik Shin ◽  
Joo-Ran Kim ◽  
Thomas E. Dever ◽  
...  
Keyword(s):  
Single Molecule ◽  
Translation Initiation ◽  
Messenger Rna ◽  
Ribosomal Subunit ◽  
Mrna Translation ◽  
Start Codon ◽  
Structural Basis ◽  
Large Ribosomal Subunit ◽  
Reading Frame ◽  
Fluorescence Measurements

Abstract Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.

scholarly journals Genetic removal of p70 S6K1 corrects coding sequence length-dependent alterations in mRNA translation in fragile X syndrome mice

2021 ◽  
Vol 118 (18) ◽  
pp. e2001681118
Author(s):  
Sameer Aryal ◽  
Francesco Longo ◽  
Eric Klann
Keyword(s):  
Protein Synthesis ◽  
Fragile X Syndrome ◽  
Messenger Rna ◽  
Fragile X ◽  
Mrna Translation ◽  
Ribosome Profiling ◽  
Sequence Length ◽  
Double Knockout ◽  
Coding Sequence ◽  
Mental Retardation Protein

Loss of the fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS). FMRP is widely thought to repress protein synthesis, but its translational targets and modes of control remain in dispute. We previously showed that genetic removal of p70 S6 kinase 1 (S6K1) corrects altered protein synthesis as well as synaptic and behavioral phenotypes in FXS mice. In this study, we examined the gene specificity of altered messenger RNA (mRNA) translation in FXS and the mechanism of rescue with genetic reduction of S6K1 by carrying out ribosome profiling and RNA sequencing on cortical lysates from wild-type, FXS, S6K1 knockout, and double knockout mice. We observed reduced ribosome footprint (RF) abundance in the majority of differentially translated genes in the cortices of FXS mice. We used molecular assays to discover evidence that the reduction in RF abundance reflects an increased rate of ribosome translocation, which is captured as a decrease in the number of translating ribosomes at steady state and is normalized by inhibition of S6K1. We also found that genetic removal of S6K1 prevented a positive-to-negative gradation of alterations in translation efficiencies (RF/mRNA) with coding sequence length across mRNAs in FXS mouse cortices. Our findings reveal the identities of dysregulated mRNAs and a molecular mechanism by which reduction of S6K1 prevents altered translation in FXS.

Translational pathophysiology: a novel molecular mechanism of human disease

Blood ◽  
2000 ◽  
Vol 95 (11) ◽  
pp. 3280-3288 ◽  
Author(s):  
Mario Cazzola ◽  
Radek C. Skoda
Keyword(s):  
Human Disease ◽  
Messenger Rna ◽  
Rna Binding ◽  
Kinase Inhibitor ◽  
Rna Binding Proteins ◽  
Point Mutations ◽  
Ribosomal Subunit ◽  
Mrna Translation ◽  
Start Codon ◽  
Stem Loop

In higher eukaryotes, the expression of about 1 gene in 10 is strongly regulated at the level of messenger RNA (mRNA) translation into protein. Negative regulatory effects are often mediated by the 5′-untranslated region (5′-UTR) and rely on the fact that the 40S ribosomal subunit first binds to the cap structure at the 5′-end of mRNA and then scans for the first AUG codon. Self-complementary sequences can form stable stem-loop structures that interfere with the assembly of the preinitiation complex and/or ribosomal scanning. These stem loops can be further stabilized by the interaction with RNA-binding proteins, as in the case of ferritin. The presence of AUG codons located upstream of the physiological start site can inhibit translation by causing premature initiation and thereby preventing the ribosome from reaching the physiological start codon, as in the case of thrombopoietin (TPO). Recently, mutations that cause disease through increased or decreased efficiency of mRNA translation have been discovered, defining translational pathophysiology as a novel mechanism of human disease. Hereditary hyperferritinemia/cataract syndrome arises from various point mutations or deletions within a protein-binding sequence in the 5′-UTR of the L-ferritin mRNA. Each unique mutation confers a characteristic degree of hyperferritinemia and severity of cataract in affected individuals. Hereditary thrombocythemia (sometimes called familial essential thrombocythemia or familial thrombocytosis) can be caused by mutations in upstream AUG codons in the 5′-UTR of the TPO mRNA that normally function as translational repressors. Their inactivation leads to excessive production of TPO and elevated platelet counts. Finally, predisposition to melanoma may originate from mutations that create translational repressors in the 5′-UTR of the cyclin-dependent kinase inhibitor–2A gene.

DEGRADATION OF MESSENGER RNA IN MAMMALIAN CELLS

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S369-S380 ◽  
Author(s):  
Francis T. Kenney ◽  
Kai-Lin Lee ◽  
Charles D. Stiles
Keyword(s):  
Messenger Rna ◽  
Mammalian Cells ◽  
Messenger Rnas ◽  
Tyrosine Transaminase

ABSTRACT Analyses of the response of hydrocortisone-induced tyrosine transaminase in cultured H-35 cells to inhibitors of translation (cycloheximide, puromycin) suggest: (1) that bound ribosomes stabilize messenger RNA in vivo; (2) that messenger is degraded at a rate determined by the rate of translation. Since specific messenger RNAs of mammalian cells are degraded at quite different rates, there may be extensive heterogeneity either in the rate at which ribosomes traverse different messengers or in the number of ribosomes which translate specific messenger RNAs.

scholarly journals Inosine in Biology and Disease

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 600
Author(s):  
Sundaramoorthy Srinivasan ◽  
Adrian Gabriel Torres ◽  
Lluís Ribas de Pouplana
Keyword(s):  
Human Health ◽  
Purine Biosynthesis ◽  
Messenger Rnas ◽  
Transfer Rnas ◽  
Functional Roles ◽  
Codon Recognition ◽  
Wobble Position ◽  
Biosynthesis Gene ◽  
The Stability ◽  
Cell Signaling Pathways

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.

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