October 22nd
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Joiret et al. investigate the electric field of the catalytic centre of ribosomes using a geometrical model. Choudhary et al. explore azole resistance in Candida albicans, and finally Zhang et al. look at pgRNA translation in the hepatitis B virus (HBV).
A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics
Computational and Structural Biotechnology Journal, 2023
Joiret, M., Kerff, F., Rapino, F., Close, P. and Geris, L
The primary role of the large ribosome subunit is to facilitate the creation of peptide bonds. This chemical process occurs at a specific site called the peptidyl transferase centre (PTC). Research has shown that the effectiveness of this catalytic activity depends on the electrical properties of the environment surrounding the PTC.
In this study, the authors aimed to understand how the electric field in the ribosome’s catalytic environment affects the rate of protein synthesis, particularly when certain charged amino acids are incorporated near the end of the growing peptide chain. To investigate this, Joiret et al. have developed a simplified geometric model based on the X-ray structures of the ribonucleic cavity near the catalytic centre within the large ribosomal subunit. The goal of this model is to provide a quantitative estimation of the electrostatic potential and electric field experienced during the peptidyl transfer reaction.
This paper begins with five publicly available atomic ribosome structures from various life domains. By employing an informed deconvolution technique on the hypo-exponential distribution, it becomes possible to extract kinetic details about the three sub-steps of elongation using Ribo-Seq data. To the best of the authors’ knowledge, this marks the inaugural application of deconvolving hypo-exponential distributions, previously fitted to ribosome-normalised footprint counts on codons, for the interpretation of Ribo-Seq data. The authors’ interpretation of ribosome footprint profiles as hypo-exponential distributions enhances data analysis and parameter learning in Ribo-Seq repositories. This will facilitate future bioinformatics and machine learning research, allowing for more precise understanding of ribosomal elongation sub-steps and codon-specific ribosome dwell times across various experimental conditions and species with diverse codon preferences.
Genome-wide translational response of Candida albicans to fluconazole treatment.
Microbiology Spectrum, 2023
Choudhary, S., Mundodi, V., Smith, A.D. and Kadosh, D.
At present, there are only three primary categories of antifungal medications accessible for treating individuals with candidiasis: azoles, echinocandins, and polyenes. Azoles, the most frequently prescribed drug group, have a specific focus on the ergosterol production pathway, which is crucial for maintaining the integrity of fungal cell membranes.
The frequent use of antifungals for recurring Candida infections, alongside prolonged antibiotic use, has led to a significant increase in drug-resistant strains. While genetic mutations, chromosomal rearrangements, and transcriptional processes have been extensively studied in azole resistance, they often miss the impact of post-transcriptional and translational mechanisms on protein expression. To address this gap, the authors employ ribosome profiling to comprehensively examine Candida albicans’ translational response to fluconazole treatment.
This research uncovered novel C. albicans genome sections with strong ribosome presence and 3-nucleotide patterns that initially seemed perplexing due to the presence of stop codons, though the authors now suspect that these RNAs are polycistronic, with multiple small coding sequences. Future ribosome profiling studies should be carried out to confirm this hypothesis. Overall, the research identifies genes with significantly altered translational efficiency, encompassing various biological functions such as cell cycle, DNA repair, cell wall/membrane biosynthesis, transport, signalling, DNA- and RNA-binding activities, and protein synthesis. Comparisons between the most prominent gene categories regulated by fluconazole at translational and transcriptional levels reveal both similarities and differences. Crucially, only a small number of genes are subject to both translational and transcriptional control in this context. These findings suggest that C. albicans possess distinct translational mechanisms crucial for responding to antifungal treatment, potentially offering avenues for novel antifungal therapies.
RNA binding protein TIAR modulates HBV replication by tipping the balance of pgRNA translation
Signal Transduction and Targeted Therapy, 2023
Zhang, T., Zheng, H., Lu, D., Guan, G., Li, D., Zhang, J., Liu, S., Zhao, J., Guo, J.T., Lu, F. and Chen
The pregenomic RNA (pgRNA) of hepatitis B virus (HBV) functions not only as a bicistronic messenger RNA for the translation of core protein (Cp) and DNA polymerase (Pol) but also as the template for reverse transcriptional replication of viral DNA upon its encapsulation into the nucleocapsid. While it is widely recognised that pgRNA predominantly translates Cp over Pol, the precise molecular mechanism governing the efficiency of Cp and Pol translation from pgRNA remains poorly understood.
In this research, the authors conducted a comprehensive analysis to profile cellular proteins associated with HBV nucleocapsids and pgRNA using a variety of methods. Initially, this investigation led to the discovery of TIA-1-related protein (TIAR) as a newfound cellular protein that interacts with pgRNA and enhances HBV DNA replication.
To learn if TIAR specifically regulates pgRNA, the authors used Ribo-seq analysis and PRM-based mass spectrometry, using human hepatoma cells. Intriguingly, when the authors manipulated TIAR expression levels, it did not affect the levels of HBV transcripts or the secretion of HBsAg and HBeAg, which are markers of HBV replication. However, it was demonstrated that the depletion of TIAR led to a decrease in the initiation of Pol translation, while enhancing Cp translation. One hypothesis the authors had was that TIAR binding to the pgRNA 5′ ε stem-loop may disrupt the eIF4F complex formation at the 5′ cap of pgRNA or interfere with 80S complex assembly at the Cp ORF AUG codon.
The central discovery of this investigation, however, is the identification of TIAR and its interaction with pgRNA, boosting Pol translation, and consequently facilitating the packaging of Pol-pgRNA complexes into nucleocapsids, thus promoting HBV replication. This revelation offers valuable insights into the molecular interplay between HBV and host cells and positions TIAR as a promising therapeutic target for chronic hepatitis B.