Structure of the human MTERF4–NSUN4 protein complex that regulates mitochondrial ribosome biogenesis

Abstract

Proteins crucial for the respiratory chain are translated by the mitochondrial ribosome. Mitochondrial ribosome biogenesis is therefore critical for oxidative phosphorylation capacity and disturbances are known to cause human disease. This complex process is evolutionary conserved and involves several RNA processing and modification steps required for correct ribosomal RNA maturation. We recently showed that a member of the mitochondrial transcription termination factor (MTERF) family of proteins, MTERF4, recruits NSUN4, a 5-methylcytosine RNA methyltransferase, to the large ribosomal subunit in a process crucial for mitochondrial ribosome biogenesis. Here, we describe the 3D crystal structure of the human MTERF4-NSUN4 complex determined to 2.9 Å resolution. MTERF4 is composed of structurally repeated MTERF-motifs that form a nucleic acid binding domain. NSUN4 lacks an N-or C-terminal extension that is commonly used for RNA recognition by related RNA methyltransferases. Instead, NSUN4 binds to the C-terminus of MTERF4. A positively charged surface forms an RNA binding path from the concave to the convex side of MTERF4 and further along NSUN4 all of the way into the active site. This finding suggests that both subunits of the protein complex likely contribute to RNA recognition. The interface between MTERF4 and NSUN4 contains evolutionarily conserved polar and hydrophobic amino acids, and mutations that change these residues completely disrupt complex formation. This study provides a molecular explanation for MTERF4-dependent recruitment of NSUN4 to ribosomal RNA and suggests a unique mechanism by which other members of the large MTERF-family of proteins can regulate ribosomal biogenesis. mitochondria | translation | X-ray crystallography

Mitochondrial Ribosomal RNA (rRNA) Methyltransferase Family Members Are Positioned to Modify Nascent rRNA in Foci near the Mitochondrial DNA Nucleoid

“…At this point, we cannot be certain that our recombinant RNMTL1 or MRM1 proteins folded correctly when expressed in bacteria. If any of these proteins require additional factors to stabilize them, as seems to be the case for NSUN4-MTERF4 (19,36,37), these partners have not yet been identified. Because none of the mammalian mitochondrial RNA methyltransferase members we have expressed have robust RNA methyltransferase activity, it is also possible FIGURE 9.…”

An artificial PPR scaffold for programmable RNA recognition

“…We observed that, compared with natural PPR proteins, hydrophobic interactions organizing the overall PPR scaffold are shielded from the solvent by salt bridges between residues at position 17, 27 and 15, 18, 25. This is reminiscent of the binding between NSUN4 and MTERF1 proteins, where salt bridges also flank hydrophobic interactions to provide a very stable interaction interface 34 . In addition, consensus design enabled core structural characteristics of PPRs to be elucidated without interference from the idiosyncratic features present in individual natural proteins.…”

A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU)

“…The fact that mammalian mTERF1, mTERF3, and mTERF4 share a common fold and are structurally similar to each other, even though mTERF3 was crystallized in the absence of its substrate (Spåhr et al, 2010) and mTERF4 in complex with another protein (Spåhr et al, 2012), supports the conclusion that mTERF proteins have evolved to bind nucleic acids (Byrnes and Garcia-Diaz, 2011). However, it is becoming increasingly clear that the nucleic acid need not necessarily be doublestranded DNA (dsDNA); RNAs can also serve as targets of mTERFs.…”