bims-tricox 2023-05-07 papers

Issue of 2023–05–07
six papers selected by
Yash Verma, University of Zurich

EMBO Rep. 2023 May 02. e56910

Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.

Benjamin Lau, Zixuan Huang, Nikola Kellner, Shuangshuang Niu, Otto Berninghausen, Roland Beckmann, Ed Hurt, Jingdong Cheng.

Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.

Keywords: 5S RNP/Dbp10; pre-60S ribosome; ribosome; ribosome biogenesis

DOI: https://doi.org/10.15252/embr.202356910

bioRxiv. 2023 Apr 17. pii: 2023.04.16.537070. [Epub ahead of print]

The structure of a hibernating ribosome in a Lyme disease pathogen.

Manjuli R Sharma, Swati R Manjari, Ekansh K Agrawal, Pooja Keshavan, Ravi K Koripella, Soneya Majumdar, Ashley L Marcinkiewicz, Yi-Pin Lin, Rajendra K Agrawal, Nilesh K Banavali.

The spirochete bacterial pathogen Borrelia ( Borreliella) burgdorferi ( Bbu ) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. We determined the structure of the Bbu 70S ribosome by single particle cryo-electron microscopy (cryo-EM) at a resolution of 2.9 Å, revealing its distinctive features. In contrast to a previous study suggesting that the single hibernation promoting factor protein present in Bbu (bbHPF) may not bind to its ribosome, our structure reveals a clear density for bbHPF bound to the decoding center of the small ribosomal 30S subunit. The 30S subunit has a non-annotated ribosomal protein, bS22, that has been found only in mycobacteria and Bacteroidetes so far. The protein bL38, recently discovered in Bacteroidetes, is also present in the Bbu large 50S ribosomal subunit. The protein bL37, previously seen only in mycobacterial ribosomes, is replaced by an N-terminal α-helical extension of uL30, suggesting that the two bacterial ribosomal proteins uL30 and bL37 may have evolved from one longer uL30 protein. The longer uL30 protein interacts with both the 23S rRNA and the 5S rRNA, is near the peptidyl transferase center (PTC), and could impart greater stability to this region. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energies are predicted for antibiotics, bound to the decoding center or PTC and are in clinical use for Lyme disease, that account for subtle distinctions in antibiotic-binding regions in the Bbu ribosome structure. Besides revealing unanticipated structural and compositional features for the Bbu ribosome, our study thus provides groundwork to enable ribosome-targeted antibiotic design for more effective treatment of Lyme disease.

DOI: https://doi.org/10.1101/2023.04.16.537070

Int J Biol Macromol. 2023 May 02. pii: S0141-8130(23)01574-X. [Epub ahead of print] 124680

Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases.

Dejiu Zhang, Lei Zhu, Fei Wang, Peifeng Li, Yin Wang, Yanyan Gao.

Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.

Keywords: Eukaryotic translation; Fidelity control; Ribosome; Translational factors

DOI: https://doi.org/10.1016/j.ijbiomac.2023.124680

Wiley Interdiscip Rev RNA. 2023 May 03. e1792

Translation machinery captured in motion.

Hassan Zafar, Ahmed H Hassan, Gabriel Demo.

Translation accuracy is one of the most critical factors for protein synthesis. It is regulated by the ribosome and its dynamic behavior, along with translation factors that direct ribosome rearrangements to make translation a uniform process. Earlier structural studies of the ribosome complex with arrested translation factors laid the foundation for an understanding of ribosome dynamics and the translation process as such. Recent technological advances in time-resolved and ensemble cryo-EM have made it possible to study translation in real time at high resolution. These methods provided a detailed view of translation in bacteria for all three phases: initiation, elongation, and termination. In this review, we focus on translation factors (in some cases GTP activation) and their ability to monitor and respond to ribosome organization to enable efficient and accurate translation. This article is categorized under: Translation > Ribosome Structure/Function Translation > Mechanisms.

Keywords: cryoelectron microscopy; structural biology; translation

DOI: https://doi.org/10.1002/wrna.1792

Science. 2023 May 05. 380(6644): 531-536

Molecular basis of translation termination at noncanonical stop codons in human mitochondria.

Martin Saurer, Marc Leibundgut, Hima Priyanka Nadimpalli, Alain Scaiola, Tanja Schönhut, Richard G Lee, Stefan J Siira, Oliver Rackham, René Dreos, Tea Lenarčič, Eva Kummer, David Gatfield, Aleksandra Filipovska, Nenad Ban.

The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.

DOI: https://doi.org/10.1126/science.adf9890

Mol Cell. 2023 May 04. pii: S1097-2765(23)00250-2. [Epub ahead of print]83(9): 1374-1376

Fix it, don't trash it: Ribosome maintenance by chaperone-mediated repair of damaged subunits.

Silvan Spiri, Gloria Ann Brar.

Acute stressors or normal cellular function may result in ribosomal protein damage, which threatens the functional ribosome pool and translation. In this issue, Yang et al.1 show that chaperones can extract damaged ribosomal proteins and replace them with newly synthesized versions to repair mature ribosomes.

DOI: https://doi.org/10.1016/j.molcel.2023.04.006