Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome

Singh, Vivek P.; Itoh, Yuzuru; Huynen, Martijn A.; Amunts, Alexey

doi:10.1101/2022.06.20.496763

Cited by 12 publications

(14 citation statements)

References 88 publications

(176 reference statements)

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“…As a last test of our model, we analyzed how it performed when predicting mitochondrial protein synthesis in cells lacking LRPPRC, which associates with the ribosome and whose loss leads to disrupted polyadenylation and destabilized mt-mRNA 15,22,23 . We analyzed HEK293T cells lacking LRPPRC (LRPPRC KO ) and found that our quantitative HeLa-based model that performed well for other cell lines displayed little predictive power (Fig 6C).…”

Section: A Minimal Model Of Gene Expression Predicts Nuclear-and Mito...mentioning

confidence: 99%

“…To test our approach in a system with different turnover rates, we analyzed LRPPRC knockout and matched control cells 5 . Mutations in LRPPRC cause the French-Canadian type of Leigh syndrome, and the LRPPRC protein is involved in mt-mRNA stabilization, poly(A) tailing, and translation (Fig S1O) 5,15,23,24 . Depletion of LRPPRC had profound effects on the steady-state levels of most heavy-strand encoded RNAs, as seen previously (Fig S1P).…”

Section: Differential Mt-mrna Degradation Rates Determine the Heavy-s...mentioning

confidence: 99%

“…As turnover helps establish the mt-mRNA steady-state levels, we next wondered what is responsible for the heterogeneity in mt-mRNA half-lives. Mutations in LRPPRC cause the French Canadian type of Leigh syndrome, and the LRPPRC protein is involved in mt-mRNA stabilization, poly(A) tailing, and translation in both mice and humans (Figure 1IH) 3,15,30,31 .…”

Section: Lrpprc-controlled Rna Turnover Rates Set Mitochondrial Mrna ...mentioning

confidence: 99%

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A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

McShane

Couvillion

Ietswaart

et al. 2023

Preprint

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Mitochondria play a critical role in cellular metabolism primarily through hosting the oxidative phosphorylation (OXPHOS) machinery that is encoded by mitochondrial DNA (mtDNA) and nuclear DNA, with each genome separately regulated in their respective compartments. To unravel how the two gene expression systems collaborate to produce the OXPHOS complexes, the regulatory principles controlling the production of mtDNA-encoded proteins need to be elucidated. Here, we performed a quantitative analysis of the mitochondrial messenger RNA (mt-mRNA) life cycle to gain insight into which steps of gene expression experience the most regulatory control. Our analysis revealed a unique balance between the rapid turnover and high accumulation of mt-mRNA, leading to a 700-fold higher transcriptional output than nuclear-encoded OXPHOS genes. Additionally, we observed that mt-mRNA processing and its association with the mitochondrial ribosome occur rapidly and that these processes are linked mechanistically. These data resulted in a model of mtDNA expression that is predictive across human cell lines, revealing that differential turnover and translation efficiencies are the major contributors to mitochondrial-encoded protein synthesis. Applying this framework to a disease model of Leigh syndrome, French-Canadian type, we found that disrupting the responsible nuclear-encoded gene, LRPPRC, perturbs OXPHOS biogenesis predominantly through altering mt-mRNA stability. Our findings provide a comprehensive view of the intricate regulatory mechanisms governing mtDNA-encoded protein synthesis, highlighting the importance of quantitatively analyzing the mitochondrial RNA life cycle for decoding the regulatory principles of mtDNA expression.

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Section: A Minimal Model Of Gene Expression Predicts Nuclear-and Mito...mentioning

confidence: 99%

Section: Differential Mt-mrna Degradation Rates Determine the Heavy-s...mentioning

confidence: 99%

Section: Lrpprc-controlled Rna Turnover Rates Set Mitochondrial Mrna ...mentioning

confidence: 99%

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A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

McShane

Couvillion

Ietswaart

et al. 2023

Preprint

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“…So perhaps mTRANs evolved in land plants to compensate for increasing variability in mitochondrial ribosome binding site position, or conversely, the appearance of mTRANs allowed this variability to occur. These findings indicate that translational initiation by mitochondrial ribosomes occurs in a different way in plants as compared with in fungi and animals ( 12 , 61 ).…”

Section: Discussionmentioning

confidence: 94%

An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants

Tran,

Schmitt,

Lama

et al. 2023

Science

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Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that “mitochondrial translation factors” mTRAN1 and mTRAN2 are land plant–specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)–like RNA binding proteins of the mitoribosomal “small” subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5′ regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.

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“…The human mitoribosome has a distinct structure, it receives mRNAs with involvement of Leucine-rich PPR-motif-containing protein (LRPPRC) and synthesizes 13 respiratory chain proteins delivered to the inner mitochondrial membrane via the OXA1L insertase ( Itoh et al, 2021 ; Singh et al, 2022 ). Cryo-EM has been instrumental in the structure determination of the mitoribosome, however, the description is currently limited to mitoribosomal proteins, rRNA, and associated factors, whereas important metabolic cofactors of potential therapeutic interest are largely excluded ( Aibara et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules

Itoh

Singh

Khawaja

et al. 2022

eLife

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The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron–sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron–sulfur, and the finding of iron–sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.

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Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome

Cited by 12 publications

References 88 publications

A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis

An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants

Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules

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