de-novo-identification-actively-translated-open-reading-frames-with

<em>De novo</em> Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Identification of open reading frames (ORFs), especially those encoding small peptides and being actively translated under specific physiological ...

Tsinghua University

Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science

The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.

IDH1 fine-tunes cap-dependent translation initiation.

eIF3, a multi-subunit complex with numerous functions in canonical translation initiation, is known to interact with 40S and 60S ribosomal proteins and translation elongation factors, but a direct involvement in translation elongation has never been demonstrated. We found that eIF3 deficiency reduced early ribosomal elongation speed between codons 25 and 75 on a set of ∼2,700 mRNAs encoding proteins associated with mitochondrial and membrane functions, resulting in defective synthesis of their encoded proteins. To promote elongation, eIF3 interacts with 80S ribosomes translating the first ∼60 codons and serves to recruit protein quality-control factors, functions required for normal mitochondrial physiology. Accordingly, eIF3e mice accumulate defective mitochondria in skeletal muscle and show a progressive decline in muscle strength. Hence, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for mitochondrial physiology and muscle health.

eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health.

Ribosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools designed for dissection of the translatome from different aspects. However, as the studies of translation advance quickly, the current toolbox still falls in short, and more specialized tools are in urgent need for deeper and more efficient mining of the important and new features of the translation landscapes.

RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data.

Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina based on the fireworks algorithm, which combined the fireworks algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon local search method adopted in AutoDock Vina to address the pose search problem in docking. The FWA was used as a global optimizer to rapidly search promising poses, and the Broyden-Fletcher-Goldfarb-Shannon method was incorporated into FWAVina to perform an exact local search. FWAVina was developed and tested on the PDBbind and DUD-E datasets. The docking performance of FWAVina was compared with the original Vina program. The results showed that FWAVina achieves a remarkable execution time reduction of more than 50 % than Vina without compromising the prediction accuracies in the docking and virtual screening experiments. In addition, the increase in the number of ligand rotatable bonds has almost no effect on the efficiency of FWAVina. The higher accuracy, faster convergence and improved stability make the FWAVina method a better choice of docking tool for computer-aided drug design. The source code is available at https://github.com/eddyblue/FWAVina/.

FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm.

Cells mitigate ER stress through the unfolded protein response (UPR). Here, we report formation of ER whorls as an effector mechanism of the ER stress response. We found that strong ER stress induces formation of ER whorls, which contain ER-resident proteins such as the Sec61 complex and PKR-like ER kinase (PERK). ER whorl formation is dependent on PERK kinase activity and is mediated by COPII machinery, which facilitates ER membrane budding to form tubular-vesicular ER whorl precursors. ER whorl precursors then go through Sec22b-mediated fusion to form ER whorls. We further show that ER whorls contribute to ER stress-induced translational inhibition by possibly modulating PERK activity and by sequestering translocons in a ribosome-free environment. We propose that formation of ER whorls reflects a new type of ER stress response that controls inhibition of protein translation.

COPII mitigates ER stress by promoting formation of ER whorls.

Bacterial outer membrane (OM), an asymmetric lipid bilayer functioning as a self-protective barrier with reduced permeability for Gram-negative bacteria, yet wasting nutrients and energy to synthesize, has not been studied for its effect on bioproduction. Here we construct several OM-defected halophile Halomonas bluephagenesis strains to investigate the effects of OM on bioproduction. We achieve enhanced chassis properties of H. bluephagenesis based on positive cellular properties among several OM-defected strains. The OM-defected H. bluephagenesis WZY09 demonstrates better adaptation to lower salinity, increasing 28%, 30% and 12% on dry cell mass (DCM), poly(3-hydroxybutyrate) (PHB) accumulation and glucose to PHB conversion rate, respectively, including enlarged cell sizes and 21-folds reduced endotoxin. Interestingly, a poly(3-hydroxybutyrate-co-21mol%4-hydroxybutyrate) (P(3HB-co-21mol%4HB)) is produced by H. bluephagenesis WZY09 derivate WZY249, increasing 60% and 260% on polyhydroxyalkanoate (PHA) production and 4HB content, respectively. Furthermore, increased electroporation efficiency, more sensitive isopropyl β-D-1-thio-galactopyranoside (IPTG) induction, better oxygen uptake, enhanced antibiotics sensitivity and ectoine secretion due to better membrane permeability are observed if OM defected, demonstrating significant OM defection impacts for further metabolic engineering, synthetic biology studies and industrial applications.

Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties.

A major part of the transcriptome complexity is attributed to multiple types of DNA or RNA fusion events, which take place within a gene such as alternative splicing or between different genes such as DNA rearrangement and trans-splicing. In the present study, using the RNA deep sequencing data, we systematically survey a type of non-canonical fusions between the RNA transcripts from the two opposite DNA strands. We name the products of such fusion events cross-strand chimeric RNA (cscRNA). Hundreds to thousands of cscRNAs can be found in human normal tissues, primary cells, and cancerous cells, and in other species as well. Although cscRNAs exhibit strong tissue-specificity, our analysis identifies thousands of recurrent cscRNAs found in multiple different samples. cscRNAs are mostly originated from convergent transcriptions of the annotated genes and their anti-sense DNA. The machinery of cscRNA biogenesis is unclear, but the cross-strand junction events show some features related to RNA splicing. The present study is a comprehensive survey of the non-canonical cross-strand RNA junction events, a resource for further characterization of the originations and functions of the cscRNAs.

Article	Year
IDH1 fine-tunes cap-dependent translation initiation. Journal of molecular cell biology\| PubMed ID: 31408165	2019
eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health. Molecular cell\| PubMed ID: 32589965	2020
RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data. BMC bioinformatics\| PubMed ID: 32738892	2020
FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm. Computational biology and chemistry\| PubMed ID: 32861160	2020
COPII mitigates ER stress by promoting formation of ER whorls. Cell research\| PubMed ID: 32989223	2021
Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties. Metabolic engineering\| PubMed ID: 34098101	2021
Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts. Nature communications\| PubMed ID: 34330918	2021

Fajin Li

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