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Structure paper

TitleStructural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.
Journal, issue, pagesNat Struct Mol Biol, Vol. 31, Issue 12, Page 1838-1847, Year 2024
Publish dateAug 12, 2024
AuthorsVivek Singh / J Conor Moran / Yuzuru Itoh / Iliana C Soto / Flavia Fontanesi / Mary Couvillion / Martijn A Huynen / L Stirling Churchman / Antoni Barrientos / Alexey Amunts /
PubMed AbstractIn mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA ...In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA delivery factor and report its cryo-electron microscopy structure in complex with SLIRP (SRA stem-loop-interacting RNA-binding protein), mRNA and the mitoribosome. The structure shows that LRPPRC associates with the mitoribosomal proteins mS39 and the N terminus of mS31 through recognition of the LRPPRC helical repeats. Together, the proteins form a corridor for handoff of the mRNA. The mRNA is directly bound to SLIRP, which also has a stabilizing function for LRPPRC. To delineate the effect of LRPPRC on individual mitochondrial transcripts, we used RNA sequencing, metabolic labeling and mitoribosome profiling, which showed a transcript-specific influence on mRNA translation efficiency, with cytochrome c oxidase subunit 1 and 2 translation being the most affected. Our data suggest that LRPPRC-SLIRP acts in recruitment of mitochondrial mRNAs to modulate their translation. Collectively, the data define LRPPRC-SLIRP as a regulator of the mitochondrial gene expression system.
External linksNat Struct Mol Biol / PubMed:39134711 / PubMed Central
MethodsEM (single particle)
Resolution2.69 - 3.38 Å
Structure data

15544

8any

EMDB-15544, PDB-8any:
Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA
Method: EM (single particle) / Resolution: 2.85 Å

EMDB-16407: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on SSU head)
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-16408: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on SSU body)
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-16409: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (masked refined on SSU tail)
Method: EM (single particle) / Resolution: 3.02 Å

EMDB-16410: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on LSU body)
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-16411: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on L10/L12 stalk)
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-16412: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on mS39-LRPPRC-SLIRP)
Method: EM (single particle) / Resolution: 3.38 Å

EMDB-16413: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (focussed on central protuberance)
Method: EM (single particle) / Resolution: 2.86 Å

EMDB-16414: Human mitochondrial ribosome in complex with LRPPRC-SLIRP, A-site, P-site, E-site tRNAs and mRNA (consensus)
Method: EM (single particle) / Resolution: 2.87 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-SPM:
SPERMINE

ChemComp-SPD:
SPERMIDINE

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-VAL:
VALINE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsRIBOSOME / mitochondrial translation / mRNA delivery

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