Translation initiation landscape of tomato-infecting virus
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE160907 | GEO | 2022/05/04
REPOSITORIES: GEO
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Project description:Translation initiation landscape of tomato-infecting virus
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Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. Most of the newly identified ORFs are small and difficult to detect with in silico methods. We also identified over thirteen hundreds of upstream ORFs on annotated genes. This data could facilitate gene annotation. Besides, this data also demonstrated that uORFs, miRNAs and antisense RNAs are regulating the expression of associated genes. This study uncovered mechanisms of translational regulation and gene annotation in tomato.
2019-07-05 | GSE124962 | GEO
Project description:Cellular stress is often accompanied by non-canonical initiation of translation at alternate start codons in mammalian cells. Here we systematically investigate the extent and impact of alternate translation initiation in the context of influenza virus infection. We use ribosome profiling with the initiation inhibitor lactidomycin to experimentally delineate translation initiation sites in a human lung epithelial cell line infected with influenza virus.
2018-05-20 | GSE114636 | GEO
Project description:Ribo-seq with firefly luciferase optimality reporters to determine whether incomplete translation and/or inhibited translation initiation is responsible for the reduced ribosome occupancy on nonoptimal transcripts.
2022-05-16 | GSE202900 | GEO
Project description:The journey of a newly synthesized polypeptide starts in the peptidyltransferase center of the ribosome, from where it traverses the exit tunnel. The interior of the ribosome exit tunnel is neither straight nor smooth. How the ribosome dynamics in vivo is influenced by the exit tunnel is poorly understood. Genome-wide ribosome profiling in mammalian cells reveals elevated ribosome density at the start codon and surprisingly the downstream 5th codon position as well. We found that the highly focused ribosomal pausing shortly after initiation is attributed to the geometry of the exit tunnel, as deletion of the loop region from ribosome protein L4 diminishes translational pausing at the 5th codon position. Unexpectedly, the ribosome variant undergoes translational abandonment shortly after initiation, suggesting that there exists an obligatory step between initiation and elongation commitment. We propose that the post-initiation pausing of ribosomes represents an inherent signature of the translation machinery to ensure productive translation.
2021-02-17 | GSE166874 | GEO
Project description:Proteogenomics is an emerging research field yet lacking a standard method of analysis. In this article, we demonstrate the strength of proteogenomic analysis specific for N-terminal data that aims at the discovery of novel translational start sites. In summary, unidentified spectra were matched to a specific N-terminal peptide library encompassing all theoretical protein N-termini encoded in the genome. Gene prediction suggested 81 protein-coding models, of which several alternative proteoforms with unannotated protein starts. Next to the proteomic data, complementary ribosome footprinting data was generated from Arabidopsis thaliana cell cultures. Translation initiation site mapping by the ribosome footprinting data provided orthogonal evidence for 14 novel peptides identified by our proteogenomics pipeline.
2016-11-25 | GSE88790 | GEO
Project description:Tomato curly stunt virus (ToCSV) is a monopartite begomovirus infecting tomatoes in South Africa, with sequence similarity to tomato yellow leaf curl virus (TYLCV). While there are numerous reports on the mechanism of TYLCV resistance in tomato, the underlying mechanisms in the tomato-ToCSV pathosystem is still relatively unknown. The main aim of this study was to investigate and compare the global methylation profile of ToCSV in two near-isogenic tomato lines, one with a tolerant phenotype (T, NIL396) and one with a susceptible phenotype (S, NIL395). Bisulfite conversion and PCR amplification, coupled with a next-generation sequencing approach, were used to elucidate the global pattern of methylation of ToCSV cytosine residues in T and S leave tissue at 35 days post-infection (dpi). The extent of methylation was more pronounced in tolerant plants compared to susceptible plants in all sequence (CG, CHG and CHH) contexts, however, the overall methylation levels were relatively low (<3%). Notably, a significant interaction (p < 0.05) was observed between the viral genomic region and susceptible vs. tolerant status for CG methylated regions where it was observed that the 3'IR CG methylation was significantly (p < 0.05) higher than CG methylation of other genomic regions in tolerant and susceptible plants. Additionally, statistically significant (EdgeR p < 0.05) differentially methylated cytosines were located primarily in the genomic regions V2/V1 and C4/C1 of ToCSV. The relative expression, using RT-qPCR, was also employed in order to quantify the expression of various key methylation-related genes, MET1, CMT2, KYP4/SUVH4, DML2, RDM1, AGO4 and AGO6 in T vs. S plants at 35dpi. The differential expression between T and S was significant for MET1, KYP4/SUVH4 and RDM1 at p<0.05 which further supports more pronounced methylation observed in ToCSV from T plants vs. S plants. While this study provides new insights into the differences in methylation profiles of ToCSV in S vs. T tomato plants, further research is required to link tolerance and susceptibility to ToCSV.
2023-01-26 | GSE223671 | GEO
Project description:Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation
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Project description:Although ribosome-profiling and translation initiation sequencing (TI-seq) analyses have identified many noncanonical initiation codons, the precise detection of translation initiation sites (TISs) remains a challenge, mainly because of experimental artifacts of such analyses. Here we describe a new method, TISCA (TIS detection by translation Complex Analysis), for the accurate identification of TISs. TISCA proved to be more reliable for TIS detection compared with existing tools, and it identified a substantial number of near-cognate codons in Kozak-like sequence contexts. Analysis of proteomics data revealed the presence of methionine at the NH2-terminus of most proteins derived from near-cognate initiation codons. Although eukaryotic initiation factor 2 (eIF2), eIF2A, and eIF2D have previously been shown to contribute to translation initiation at near-cognate codons, we found that most noncanonical initiation events are dependent on eIF2, consistent with the initial amino acid being methionine. Comprehensive identification of TISs by TISCA should facilitate characterization of the mechanism of noncanonical initiation.
2021-07-01 | GSE174329 | GEO
Project description:Initiation factor 2 (eIF2) delivering the initiator methionine transfer RNA (Met-tRNAiMet) to the ribosome is a conserved key step in translation initiation. Argonaute (Ago) proteins were initially identified as eukaryotic translation initiation factor 2C,2 (EIF2C2). In the past 2 decades, Argonaute were extensively studied as a core component of RNA induced gene silencing, although various model raised the exact mechanism of Ago in translation repression remains elusive. Here we found Ago protein directly bind Met- tRNAiMet independent of miRNA binding, which interfere the formation of the ternary complex eIF2–GTP–Met- tRNAiMet. Ago proteins can solely inhibit protein synthesis via competing tRNAiMet with eIF2. Our findings elucidate a physical link between Ago and tRNAiMet and provide mechanistic insight into translation repression by Ago proteins.
2022-02-01 | GSE181004 | GEO