bims-tricox 2022-08-14 papers

Genome Biol. 2022 Aug 09. 23(1): 170

Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes.

Iliana Soto, Mary Couvillion, Katja G Hansen, Erik McShane, J Conor Moran, Antoni Barrientos, L Stirling Churchman.

BACKGROUND: Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome.
RESULTS: We resolve features of mitochondrial translation initiation and identify a small ORF in the 3' UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways.
CONCLUSIONS: Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.

DOI: https://doi.org/10.1186/s13059-022-02732-9

Cells. 2022 Aug 02. pii: 2381. [Epub ahead of print]11(15):

Differential Paralog-Specific Expression of Multiple Small Subunit Proteins Cause Variations in Rpl42/eL42 Incorporation in Ribosome in Fission Yeast.

Wenzhu Li, Jing Zhang, Wenpeng Cheng, Yuze Li, Jinwen Feng, Jun Qin, Xiangwei He.

Ribosomes within a cell are commonly viewed as biochemically homogenous RNA-protein super-complexes performing identical functions of protein synthesis. However, recent evidence suggests that ribosomes may be a more dynamic macromolecular complex with specialized roles. Here, we present extensive genetic and molecular evidence in the fission yeast S. pombe that the paralogous genes for many ribosomal proteins (RPs) are functionally different, despite that they encode the same ribosomal component, often with only subtle differences in the sequences. Focusing on the rps8 paralog gene deletions rps801d and rps802d, we showed that the mutant cells differ in the level of Rpl42p in actively translating ribosomes and that their phenotypic differences reside in the Rpl42p level variation instead of the subtle protein sequence difference between Rps801p and Rps802p. Additional 40S ribosomal protein paralog pairs also exhibit similar phenotypic differences via differential Rpl42p levels in actively translating ribosomes. Together, our work identifies variations in the Rpl42p level as a potential form of ribosome heterogeneity in biochemical compositions and suggests a possible connection between large and small subunits during ribosome biogenesis that may cause such heterogeneity. Additionally, it illustrates the complexity of the underlying mechanisms for the genetic specificity of ribosome paralogs.

Keywords: ribosome concentration model; ribosome heterogeneity; ribosome paralogs specificity

DOI: https://doi.org/10.3390/cells11152381

Trends Biochem Sci. 2022 Aug 09. pii: S0968-0004(22)00187-6. [Epub ahead of print]

Cooperative assembly of the mitochondrial respiratory chain.

Erika Fernández-Vizarra, Cristina Ugalde.

Deep understanding of the pathophysiological role of the mitochondrial respiratory chain (MRC) relies on a well-grounded model explaining how its biogenesis is regulated. The lack of a consistent framework to clarify the modes and mechanisms governing the assembly of the MRC complexes and supercomplexes (SCs) works against progress in the field. The plasticity model was postulated as an attempt to explain the coexistence of mammalian MRC complexes as individual entities and associated in SC species. However, mounting data accumulated throughout the years question the universal validity of the plasticity model as originally proposed. Instead, as we argue here, a cooperative assembly model provides a much better explanation to the phenomena observed when studying MRC biogenesis in physiological and pathological settings.

Keywords: assembly factors; cooperative assembly model; mitochondria; plasticity model; respiratory chain organization; supercomplexes

DOI: https://doi.org/10.1016/j.tibs.2022.07.005

G3 (Bethesda). 2022 Aug 09. pii: jkac201. [Epub ahead of print]

A set of Saccharomyces cerevisiae integration vectors for fluorescent dye labeling of proteins.

Inwha Baek, Sarah N Le, Jongcheol Jeon, Yujin Chun, Charlotte Reed, Stephen Buratowski.

Protein fusions are frequently used for fluorescence imaging of individual molecules, both in vivo and in vitro. The SNAP, CLIP, HALO (aka HaloTag7), and DHFR protein tags can be linked to small molecule dyes that provide brightness and photo-stability superior to fluorescent proteins. To facilitate fluorescent dye tagging of proteins in the yeast Saccharomyces cerevisiae, we constructed a modular set of vectors with various combinations of labeling protein tags and selectable markers. These vectors can be used in combination to create strains where multiple proteins labeled with different colored dyes can be simultaneously observed.

Keywords: CLIP; DHFR; Halo7; SNAP; Saccharomyces cerevisiae; epitope tagging; fluorescence microscopy; integration vector

DOI: https://doi.org/10.1093/g3journal/jkac201