bims-tricox 2023-12-24 papers

Issue of 2023–12–24
five papers selected by
Yash Verma, University of Zurich

Biochemistry (Mosc). 2023 Nov;88(11): 1832-1843

Diversity and Evolution of Mitochondrial Translation Apparatus.

Mariya V Baleva, Ulyana E Piunova, Ivan V Chicherin, Sergey A Levitskii, Piotr A Kamenski.

The evolution of mitochondria has proceeded independently in different eukaryotic lines, which is reflected in the diversity of mitochondrial genomes and mechanisms of their expression in eukaryotic species. Mitochondria have lost most of bacterial ancestor genes by transferring them to the nucleus or eliminating them. However, mitochondria of almost all eukaryotic cells still retain relatively small genomes, as well as their replication, transcription, and translation apparatuses. The dependence on the nuclear genome, specific features of mitochondrial transcripts, and synthesis of highly hydrophobic membrane proteins in the mitochondria have led to significant changes in the translation apparatus inherited from the bacterial ancestor, which retained the basic structure necessary for protein synthesis but became more specialized and labile. In this review, we discuss specific properties of translation initiation in the mitochondria and how the evolution of mitochondria affected the functions of main factors initiating protein biosynthesis in these organelles.

Keywords: mitochondria; regulation of translation; translation; translation initiation factors

DOI: https://doi.org/10.1134/S0006297923110135

Nucleic Acids Res. 2023 Dec 19. pii: gkad1206. [Epub ahead of print]

The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis.

Valentin Mitterer, Hussein Hamze, Natalia Kunowska, Ulrich Stelzl, Anthony K Henras, Ed Hurt.

During ribosome biogenesis a plethora of assembly factors and essential enzymes drive the unidirectional maturation of nascent pre-ribosomal subunits. The DEAD-box RNA helicase Dbp10 is suggested to restructure pre-ribosomal rRNA of the evolving peptidyl-transferase center (PTC) on nucleolar ribosomal 60S assembly intermediates. Here, we show that point mutations within conserved catalytic helicase-core motifs of Dbp10 yield a dominant-lethal growth phenotype. Such dbp10 mutants, which stably associate with pre-60S intermediates, impair pre-60S biogenesis at a nucleolar stage prior to the release of assembly factor Rrp14 and stable integration of late nucleolar factors such as Noc3. Furthermore, the binding of the GTPase Nug1 to particles isolated directly via mutant Dbp10 bait proteins is specifically inhibited. The N-terminal domain of Nug1 interacts with Dbp10 and the methyltransferase Spb1, whose pre-60S incorporation is also reduced in absence of functional Dbp10 resulting in decreased methylation of 25S rRNA nucleotide G2922. Our data suggest that Dbp10's helicase activity generates the necessary framework for assembly factor docking thereby permitting PTC rRNA methylation and the progression of pre-60S maturation.

DOI: https://doi.org/10.1093/nar/gkad1206

Trends Endocrinol Metab. 2023 Dec 15. pii: S1043-2760(23)00243-6. [Epub ahead of print]

Mitochondrial quality control pathways sense mitochondrial protein import.

Laurie P Lee-Glover, Timothy E Shutt.

Mitochondrial quality control (MQC) mechanisms are required to maintain a functional proteome, which enables mitochondria to perform a myriad of important cellular functions from oxidative phosphorylation to numerous other metabolic pathways. Mitochondrial protein homeostasis begins with the import of over 1000 nuclear-encoded mitochondrial proteins and the synthesis of 13 mitochondrial DNA-encoded proteins. A network of chaperones and proteases helps to fold new proteins and degrade unnecessary, damaged, or misfolded proteins, whereas more extensive damage can be removed by mitochondrial-derived vesicles (MDVs) or mitochondrial autophagy (mitophagy). Here, focusing on mechanisms in mammalian cells, we review the importance of mitochondrial protein import as a sentinel of mitochondrial function that activates multiple MQC mechanisms when impaired.

Keywords: mitochondria; mitochondrial protein import; mitochondrial quality control; mitochondrial unfolded protein response; mitochondrial-derived vesicles; mitophagy

DOI: https://doi.org/10.1016/j.tem.2023.11.004

IUBMB Life. 2023 Dec 20.

Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks.

Nhu Dinh, Nathalie Bonnefoy.

Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.

Keywords: OXPHOS complexes; PPR proteins; Schizosaccharomyces pombe; gene expression; gene fusions; mitochondrial biogenesis; mitoribosome

DOI: https://doi.org/10.1002/iub.2801

STAR Protoc. 2023 Dec 18. pii: S2666-1667(23)00757-8. [Epub ahead of print]5(1): 102790

Protocol for live-cell super-resolution imaging of transport of pre-ribosomal subunits through the nuclear pore complex.

Mark Tingey, Samuel L Junod, Coby Rush, Weidong Yang.

Here, we present a protocol for single-molecule super-resolution imaging of the nuclear export of pre-ribosomal subunits pre-40S and pre-60S through nuclear pore complexes. We describe steps for plating cells and co-transfecting cells. We then detail steps for using single-point edge-excitation sub-diffraction microscopy, allowing visualization of real-time dynamics of the pre-ribosomal subunits. For complete details on the use and execution of this protocol, please refer to Junod et al. (2023).1.

Keywords: Biophysics; Cell Biology; Cell Membrane; Microscopy; Single-molecule Assays

DOI: https://doi.org/10.1016/j.xpro.2023.102790