# Mechanism of mitoribosomal small subunit biogenesis and preinitiation

**Authors:** Yuzuru Itoh, Anas Khawaja, Ivan Laptev, Miriam Cipullo, Ilian Atanassov, Petr Sergiev, Joanna Rorbach, Alexey Amunts

PMC · DOI: 10.1038/s41586-022-04795-x · Nature · 2022-06-08

## TL;DR

This study reveals how mitoribosomal small subunits are assembled step-by-step and how this process connects to the start of protein synthesis in mitochondria.

## Contribution

The paper presents a novel sequential mechanism of mitoribosomal small subunit biogenesis and its link to translation initiation.

## Key findings

- TFB1M binds to partially unfolded rRNA h45, facilitated by RBFA, blocking the mRNA channel.
- METTL15 promotes rRNA maturation and a conformational change in RBFA, enabling mtIF3 to bind.
- mS37 outcompetes RBFA to complete the SSU–mS37–mtIF3 complex, linking assembly to initiation.

## Abstract

Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU–mS37–mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.

Structural analysis of several small mitoribosomal subunit intermediates reveals a sequential mechanism of biogenesis, and how assembly links to initiation to form active mitoribosomes.

## Linked entities

- **Proteins:** TFB1M (transcription factor B1, mitochondrial), RBFA (ribosome binding factor A), METTL15 (methyltransferase 15, mitochondrial 12S rRNA N4-cytidine), MTIF3 (mitochondrial translational initiation factor 3), MTIF2 (mitochondrial translational initiation factor 2), CHCHD1 (coiled-coil-helix-coiled-coil-helix domain containing 1)

## Full-text entities

- **Genes:** DIMT1 (DIM1 rRNA methyltransferase and ribosome maturation factor) [NCBI Gene 27292] {aka DIM1, DIMT1L, HSA9761, HUSSY5}, SDHA (succinate dehydrogenase complex flavoprotein subunit A) [NCBI Gene 6389] {aka CMD1GG, FP, MC2DN1, NDAXOA, PGL5, PPGL5}, ND4 (NADH dehydrogenase subunit 4) [NCBI Gene 4538] {aka MTND4}, COX1 (cytochrome c oxidase subunit I) [NCBI Gene 4512] {aka COI, MTCO1}, METTL15 (methyltransferase 15, mitochondrial 12S rRNA N4-cytidine) [NCBI Gene 196074] {aka METT5D1}, Mtif3 (mitochondrial translational initiation factor 3) [NCBI Gene 76366] {aka 2810012L14Rik}, SUMO1 (small ubiquitin like modifier 1) [NCBI Gene 7341] {aka DAP1, GMP1, OFC10, PIC1, SMT3, SMT3C}, GTF2H1 (general transcription factor IIH subunit 1) [NCBI Gene 2965] {aka BTF2, P62, TFB1, TFIIH}, TFB1M (transcription factor B1, mitochondrial) [NCBI Gene 51106] {aka CGI-75, CGI75, mtTFB, mtTFB1}, RBFA (ribosome binding factor A) [NCBI Gene 79863] {aka C18orf22, HsT169}, Mettl15 (methyltransferase like 15) [NCBI Gene 76894] {aka 0610027B03Rik, Mett5d1}, MTIF3 (mitochondrial translational initiation factor 3) [NCBI Gene 219402] {aka IF3mt}, GTPBP10 (GTP binding protein 10) [NCBI Gene 85865] {aka ObgH2, UG0751c10}, TRMT2B (tRNA methyltransferase 2B) [NCBI Gene 79979] {aka CXorf34, dJ341D10.3}, SSUH2 (ssu-2 homolog) [NCBI Gene 51066] {aka C3orf32, DTDP1C, SSU-2, fls485}, OXA1L (OXA1L mitochondrial inner membrane insertase) [NCBI Gene 5018] {aka OXA1, OXA1L1}, MALSU1 (mitochondrial assembly of ribosomal large subunit 1) [NCBI Gene 115416] {aka C7orf30, mtRsfA}, TRNG (tRNA-Gly) [NCBI Gene 4563] {aka MTTG}, NDUFAB1 (NADH:ubiquinone oxidoreductase subunit AB1) [NCBI Gene 4706] {aka ACP, ACP1, FASN2A, SDAP}, EIF5B (eukaryotic translation initiation factor 5B) [NCBI Gene 9669] {aka IF2}, Rbfa (ribosome binding factor A) [NCBI Gene 68731] {aka 1110032A13Rik}, MRM3 (mitochondrial rRNA methyltransferase 3) [NCBI Gene 55178] {aka RMTL1, RNMTL1}, Ms37 (minisatellites detected by probe MMS37) [NCBI Gene 108471] {aka MMS37}, RPL12 (ribosomal protein L12) [NCBI Gene 6136] {aka L12, uL11}, Trmt2b (TRM2 tRNA methyltransferase 2B) [NCBI Gene 215201] {aka 4732479N06Rik}, MTIF2 (mitochondrial translational initiation factor 2) [NCBI Gene 4528]
- **Diseases:** LSU (MESH:C580233), developmental disorders (MESH:D002658), embryonic lethal (MESH:D020964), cardiomyopathy (MESH:D009202)
- **Chemicals:** EGTA (MESH:D004533), penicillin (MESH:D010406), I (MESH:D007455), Sucrose (MESH:D013395), streptomycin (MESH:D013307), emetine (MESH:D004640), HCl (MESH:D006851), acetonitrile (MESH:C032159), Zeocin (MESH:C105427), pyrimidine (MESH:C030986), ethanol (MESH:D000431), CO2 (MESH:D002245), uridine (MESH:D014529), chloroacetamide (MESH:C013874), Lys (MESH:D008239), MgCl2 (MESH:D015636), HEPES (MESH:D006531), hygromycin (MESH:C026273), 4'-phosphopantetheine (MESH:C003129), Triton X-100 (MESH:D017830), tetracycline (MESH:D013752), KCl (MESH:D011189), cysteine (MESH:D003545), puromycin (MESH:D011691), 5-methyluridine (MESH:C009182), copper (MESH:D003300), methanol (MESH:D000432), nitrogen (MESH:D009584), EMD-13561 (-), Coomassie blue (MESH:C048139), formic acid (MESH:C030544), acetic acid (MESH:D019342), Methionine (MESH:D008715), Hydrogens (MESH:D006859), Water (MESH:D014867), 13C (MESH:C000615229), mannitol (MESH:D008353), 35S (MESH:C000615320), PBS (MESH:D007854), NaCl (MESH:D012965), GTP (MESH:D006160), n-dodecyl beta-d-maltoside (MESH:C040358), Amino acids (MESH:D000596), carbon (MESH:D002244), glycerol (MESH:D005990), 5-formylcytidine (MESH:C086073), DTT (MESH:D004229), laurate (MESH:D007848), ice (MESH:D007053), Metal (MESH:D008670), fatty acid (MESH:D005227), S-adenosylhomocysteine (MESH:D012435), Asp (MESH:D001224), blasticidin (MESH:C004500), SDS (MESH:D012967), doxycycline (MESH:D004318), EDTA (MESH:D004492), GlutaMAX (MESH:C054122), PVDF (MESH:C024865), ethane (MESH:D004980)
- **Species:** Thermus thermophilus (species) [taxon 274], Mycoplasma (genus) [taxon 2093], Mus musculus (house mouse, species) [taxon 10090], Escherichia coli (E. coli, species) [taxon 562], Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** pcDN5 — Mus musculus (Mouse), Transformed cell line (CVCL_5U93), NS0 — Mus musculus (Mouse), Mouse multiple myeloma, Cancer cell line (CVCL_3940), mS37KO — Homo sapiens (Human), Lung small cell carcinoma, Cancer cell line (CVCL_IQ54), mS37RESCUE — Homo sapiens (Human), Dilated cardiomyopathy-1DD, Induced pluripotent stem cell (CVCL_A9YR), Flp-In — Cricetulus griseus (Chinese hamster), Spontaneously immortalized cell line (CVCL_U424), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), SSU-3 — Homo sapiens (Human), Ewing sarcoma, Cancer cell line (CVCL_IV95)

## Full text

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## Figures

16 figures with captions in the complete paper: https://tomesphere.com/paper/PMC9200640/full.md

## References

55 references — full list in the complete paper: https://tomesphere.com/paper/PMC9200640/full.md

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Source: https://tomesphere.com/paper/PMC9200640