MTIF3 (Q9H2K0), human mitochondrial translation initiation factor 3 (IF3mt)

Identity check

The symbol, UniProt record and domains all agree. UniProt Q9H2K0 is "Translation initiation factor IF-3, mitochondrial" (gene MTIF3, ORF name DC38), a member of the IF-3 family. Its InterPro domains are the bacterial-type IF3 N-terminal and C-terminal domains (IPR019814, IPR036787, IPR036788, IPR001288). The literature below concerns this same protein, so I found no ambiguity. Sources are in the list at the end.

I ran only two web searches. I did not read the primary papers' full text. Details that come only from search summaries are flagged as secondary.

Primary function

MTIF3 is a ribosome-binding translation initiation factor that acts on the mitochondrial small (28S) subunit. It is the mitochondrial counterpart of bacterial IF3.

• UniProt function statement. IF-3 binds the 28S subunit and shifts the equilibrium between 55S ribosomes and their 39S and 28S subunits toward the free subunits. This raises the availability of 28S subunits on which initiation begins. The statement cites the original identification paper, PMID:12095986, "Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs." That paper is in the UniProt flat file for this protein. I did not retrieve its text, and the web search did not surface it.
• Not an enzyme. There is no catalytic activity. MTIF3 acts as a ribosome-associated factor that does the following:
• It acts as an anti-association factor that dissociates 55S monosomes into 28S and 39S subunits.
• It destabilises initiator tRNA in the absence of mRNA, which supports fidelity in initiation-complex formation.
• It may help recruit leaderless mRNAs, a feature of mammalian mitochondrial transcripts.

Structural evidence

• Cryo-EM of 28S–IF3mt (2019). Koripella et al. solved cryo-EM structures of the mammalian 28S subunit bound to human IF3mt at 3.3–3.5 Å (PMID:30677741(https://pubmed.ncbi.nlm.nih.gov/30677741/), iScience 2019). The reported findings were:
• Unique contacts between the 28S subunit and the IF3mt N-terminal domain explain its unusually high affinity for 28S.
• The mitochondria-specific C-terminal extension offers a mechanism for destabilising initiator tRNA when no mRNA is present.
• The C-terminal domain may help recruit leaderless mRNAs.
• These points come from the search summary of the abstract. I did not read the full text.
• Assembly of the initiation complex (2020). A later study reported two findings (Nat Commun, s41467-020-16503-2):
• Interactions between the mitochondria-specific protein mS37 and mtIF3 keep the small subunit in a conformation that favours later accommodation of mtIF2.
• Association of the large subunit is required for initiator tRNA and leaderless mRNA recruitment, which gives a stable initiation complex.
• Family domain architecture. The bacterial-like N- and C-terminal domains are connected by a linker. The mitochondrial protein has terminal extensions around this core. A secondary aggregator says it was identified from ESTs as a 278-aa protein (affinage.wi.mit.edu). I could not confirm this against the original paper.

Localization

• MTIF3 is a nuclear-encoded protein that is imported into the mitochondrial matrix, where it works on mitoribosomes. UniProt marks the sequence as a precursor, so it carries a cleavable N-terminal mitochondrial targeting presequence.
• UniProt cites an N-terminome study of the human mitochondrial proteome (PMID:25944712) for presequence processing.
• Its site of action is the mitochondrial matrix, specifically the mitochondrial small ribosomal subunit and the initiation complex.

Pathway

MTIF3 works in mitochondrial translation initiation. In outline:

1. IF3mt binds free 28S subunits and prevents premature association with 39S.
2. mtIF2 (MTIF2), mRNA and fMet-tRNA join the 28S subunit.
3. IF3mt is released, and the 39S subunit joins to form the 55S initiation complex.

The mitochondrial-DNA-encoded OXPHOS subunits (13 proteins in human) are the products. Loss of MTIF3 therefore mainly affects respiratory chain and ATP synthase biogenesis.

Phenotypic and disease evidence

These findings concern the consequences of MTIF3 perturbation. They are secondary to the core function.

• Adipocyte function and obesity genetics. MTIF3 is a well-replicated obesity-associated locus. Huang et al. reported that rs67785913 is a causal cis-eQTL for MTIF3 expression. The rs67785913 CTCT allele increased MTIF3 expression in CRISPR-edited cells and enhanced transcription in a luciferase assay (eLife 2023; PMC10023155). MTIF3 deficiency in human white adipocytes had these effects:
• It reduced mitochondrial respiration and endogenous fatty acid oxidation.
• It altered expression of mtDNA-encoded genes and proteins.
• It disturbed OXPHOS complex assembly.
• After glucose restriction, knockout cells retained more triglycerides than controls.
• Other models (from the same search summary, not primary reads):
• In HepG2 cells, MTIF3 loss decreased translation of the mtDNA-encoded ATP6 mRNA without affecting proliferation.
• In mice, heart- and skeletal-muscle-specific loss of MTIF3 caused cardiomyopathy. It also produced increased but uncoordinated mitochondrial protein synthesis and loss of specific respiratory complexes.
• I did not retrieve the primary citations for these, so verify them before using them in a review.
• No total-deficiency human disease. The eLife authors note that no human genomic mutations causing total MTIF3 deficiency have been reported.

Notes for curation

• Interaction list. The UniProt INTERACTION list (APOD, BCL2L1, CD47, LDLR and others, all NbExp=3) comes from a single high-throughput IntAct dataset. These are mostly membrane or secreted proteins that do not share a compartment with MTIF3, so they should not support any functional annotation.
• Core GO-relevant statements. I would phrase them as follows. The first two are well supported by the structural and UniProt evidence. The third depends on a mechanism that is plausible but not firmly established.
• Molecular function: mitochondrial small ribosomal subunit (28S) binding, with an anti-association role and a role in positioning initiator tRNA. Avoid "protein binding".
• Process: mitochondrial translational initiation.
• Location: mitochondrial matrix, on the 28S subunit and mitoribosome. The core function is hypothesised to be translation initiation factor activity, which is inferred from the bacterial IF3 family and the structures.
• Verification still needed. Obtain the full text of PMID:12095986 and PMID:30677741 to check the specific experimental claims before quoting them.

Sources

• Koripella et al. 2019, structure of human IF3mt bound to the 28S subunit, PMID:30677741
• Nature Communications 2020, mS37–mtIF3 and mtIF2 accommodation
• Huang et al., eLife 2023, MTIF3 eQTL and adipocyte function
• Same study, PMC10023155
• Same study, bioRxiv preprint 2022
• MTIF3 gene summary, affinage.wi.mit.edu (secondary)
• UniProt Q9H2K0 flat file, local copy in genes/human/MTIF3/MTIF3-uniprot.txt. It cites PMID:12095986 and PMID:25944712.

Citations

1. https://pubmed.ncbi.nlm.nih.gov/30677741/
2. https://link.springer.com/10.1038/s41467-020-16503-2
3. https://affinage.wi.mit.edu/gene/MTIF3
4. https://elifesciences.org/articles/84168
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10023155/
6. https://www.biorxiv.org/content/10.1101/2022.10.16.512435.full.pdf