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@article{,

title = {Biophysical Studies of the Binding of Viral RNA with the 80S Ribosome Using switchSENSE},

author = {E Schenckbecher and G Bec and T Sakamoto and B Meyer and E Ennifar},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33877606},

doi = {10.1007/978-1-0716-1197-5_15},

isbn = {33877606},

year  = {2021},

date = {2021-01-01},

journal = {Methods Mol Biol},

volume = {2263},

pages = {341-350},

abstract = {Translation initiation, in both eukaryotes and bacteria, requires essential elements such as mRNA, ribosome, initiator tRNA, and a set of initiation factors. For each domain of life, canonical mechanisms and signals are observed to initiate protein synthesis. However, other initiation mechanism can be used, especially in viral mRNAs. Some viruses hijack cellular machinery to translate some of their mRNAs through a noncanonical initiation pathway using internal ribosome entry site (IRES), a highly structured RNAs which can directly recruit the ribosome with a restricted set of initiation factors, and in some cases even without cap and initiator tRNA. In this chapter, we describe the use of biosensors relying on electro-switchable nanolevers using the switchSENSE((R)) technology, to investigate kinetics of the intergenic (IGR) IRES of the cricket paralysis virus (CrPV) binding to 80S yeast ribosome. This study provides a proof of concept for the application of this method on large complexes.},

note = {1940-6029 (Electronic) 

1064-3745 (Linking) 

Journal Article},

keywords = {Biophysics, ENNIFAR, Kinetics, Ribosome, RNA, switchSENSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Abaeva2020,

title = {The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism },

author = {I S Abaeva and Q Vicens and A Bochler and H Soufari and A Simonetti and T V Pestova and Y Hashem and C U T Hellen},

url = {https://pubmed.ncbi.nlm.nih.gov/33296660/},

doi = {10.1016/j.celrep.2020.108476 },

year  = {2020},

date = {2020-12-08},

journal = {Cell Reports},

volume = {33},

number = {10},

pages = {108476},

abstract = {Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI. },

keywords = {Cricket paralysis virus, Dicistrovirus, ENNIFAR, Halastavi árva virus; IRES, intergenic region, internal ribosomal entry site, pseudoknot, Ribosome, SERBP1, SERPINE1 mRNA binding protein 1, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Despons2020,

title = {How Many Messenger RNAs Can Be Translated by the START Mechanism? },

author = {L Despons and F Martin

},

url = {https://pubmed.ncbi.nlm.nih.gov/33171614/},

doi = {10.3390/ijms21218373 },

year  = {2020},

date = {2020-11-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {21},

pages = {8373},

abstract = {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. },

keywords = {ERIANI, LESCURE, mRNA, Ribosome, secondary structures, START, translation initiation, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{dobrenel_arabidopsis_2016,

title = {The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6.},

author = {Thomas Dobrenel and Eder Mancera-Martínez and Céline Forzani and Marianne Azzopardi and Marlène Davanture and Manon Moreau and Mikhail Schepetilnikov and Johana Chicher and Olivier Langella and Michel Zivy and Christophe Robaglia and Lyubov A Ryabova and Johannes Hanson and Christian Meyer},

doi = {10.3389/fpls.2016.01611},

issn = {1664-462X 1664-462X 1664-462X},

year  = {2016},

date = {2016-01-01},

journal = {Frontiers in plant science},

volume = {7},

pages = {1611},

abstract = {Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.},

keywords = {Phosphorylation, plastid, PPSE, proteomic, Ribosome, RPS6, TOR kinase, transcriptomic, translatomic},

pubstate = {published},

tppubtype = {article}

}