bims-tricox 2023-09-03 papers

Issue of 2023–09–03
four papers selected by
Yash Verma, University of Zurich

Nat Struct Mol Biol. 2023 Aug 31.

KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion.

Jingyu Sun, Laurel F Kinman, Dushyant Jahagirdar, Joaquin Ortega, Joseph H Davis.

Ribosome assembly is orchestrated by many assembly factors, including ribosomal RNA methyltransferases, whose precise role is poorly understood. Here, we leverage the power of cryo-EM and machine learning to discover that the E. coli methyltransferase KsgA performs a 'proofreading' function in the assembly of the small ribosomal subunit by recognizing and partially disassembling particles that have matured but are not competent for translation. We propose that this activity allows inactive particles an opportunity to reassemble into an active state, thereby increasing overall assembly fidelity. Detailed structural quantifications in our datasets additionally enabled the expansion of the Nomura assembly map to highlight rRNA helix and r-protein interdependencies, detailing how the binding and docking of these elements are tightly coupled. These results have wide-ranging implications for our understanding of the quality-control mechanisms governing ribosome biogenesis and showcase the power of heterogeneity analysis in cryo-EM to unveil functionally relevant information in biological systems.

DOI: https://doi.org/10.1038/s41594-023-01078-5

Nat Commun. 2023 Aug 26. 14(1): 5220

Assembly landscape for the bacterial large ribosomal subunit.

Kai Sheng, Ning Li, Jessica N Rabuck-Gibbons, Xiyu Dong, Dmitry Lyumkis, James R Williamson.

Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions.

DOI: https://doi.org/10.1038/s41467-023-40859-w

Am J Physiol Cell Physiol. 2023 Aug 29.

Mitochondrial Microproteins: Critical Regulators of Protein Import, Energy Production, Stress Response Pathways, and Programmed Cell Death.

Michael L Kamradt, Catherine A Makarewich.

Mitochondria rely upon the coordination of protein import, protein translation, and proper functioning of oxidative phosphorylation (OXPHOS) complexes I-V to sustain the activities of life for an organism. Each process is dependent upon the function of profoundly large protein complexes found in the mitochondria (TOMM complex, TIMM complex, OXPHOS complexes, mitoribosomes). These massive protein complexes, in some instances more than one megadalton, are built up from numerous protein subunits of varying sizes, including many proteins that are ≤100-150 amino acids. However, these small proteins, termed microproteins, not only act as cogs in large molecular machines; they also have important steps in inhibiting or promoting the intrinsic pathway of apoptosis, coordinate responses to cellular stress and even act as hormones. This review focuses on microproteins that occupy the mitochondria and are critical for its function. Although the microprotein field is relatively new, researchers have long recognized the existence of these mitochondrial proteins as critical components of virtually all aspects of mitochondrial biology. Thus, recent studies estimating that hundreds of new microproteins of unknown function exist and are missing from current genome annotations suggests that the mitochondrial "microproteome" is a rich area for future biological investigation.

Keywords: cell stress; microproteins; mitochondria; mitochondrial protein import; oxidative phosphorylation

DOI: https://doi.org/10.1152/ajpcell.00189.2023

Cell Metab. 2023 Aug 22. pii: S1550-4131(23)00289-9. [Epub ahead of print]

Preserved respiratory chain capacity and physiology in mice with profoundly reduced levels of mitochondrial respirasomes.

Dusanka Milenkovic, Jelena Misic, Johannes F Hevler, Thibaut Molinié, Injae Chung, Ilian Atanassov, Xinping Li, Roberta Filograna, Andrea Mesaros, Arnaud Mourier, Albert J R Heck, Judy Hirst, Nils-Göran Larsson.

The mammalian respiratory chain complexes I, III2, and IV (CI, CIII2, and CIV) are critical for cellular bioenergetics and form a stable assembly, the respirasome (CI-CIII2-CIV), that is biochemically and structurally well documented. The role of the respirasome in bioenergetics and the regulation of metabolism is subject to intense debate and is difficult to study because the individual respiratory chain complexes coexist together with high levels of respirasomes. To critically investigate the in vivo role of the respirasome, we generated homozygous knockin mice that have normal levels of respiratory chain complexes but profoundly decreased levels of respirasomes. Surprisingly, the mutant mice are healthy, with preserved respiratory chain capacity and normal exercise performance. Our findings show that high levels of respirasomes are dispensable for maintaining bioenergetics and physiology in mice but raise questions about their alternate functions, such as those relating to the regulation of protein stability and prevention of age-associated protein aggregation.

Keywords: OXPHOS; mitochondria; mitochondrial respirasomes; supercomplexes

DOI: https://doi.org/10.1016/j.cmet.2023.07.015