LRPPRC forms a complex with SLIRP via a PPR-RRM protein interface and mediates folding of the mitochondrial transcriptome
Henrik Spåhr1, Stefan J. Siira2, Xinping Li3, Ilian Atanassov3, Anne-Marie J. Shearwood2, Benedetta Ruzzenente4, Oliver Rackham2, Aleksandra Filipovska2 and Nils-Göran Larsson1
1Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany.
2Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia.
3Proteomics Core Facility, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany.
4Inserm U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, 75015 Paris,,France.
LRPPRC was originally identified when a mutation in its gene was shown to cause a rare French-Canadian variant of Leigh syndrome with a cytochrome c oxidase deficiency. Further characterization showed that LRPPRC acts at the post-transcriptional level to stabilize mitochondrial mRNAs and their poly(A) tails and coordinate mitochondrial translation. Over 30 pentatricopeptide repeat (PPR) RNA-binding motifs build up the all alpha-helical LRPPRC making it one of the most PPR-motif rich proteins in this family. LRPPRC forms a complex with the much smaller SLIRP that harbors a single RNA recognition motif (RRM) domain.
As a first step towards a structural understanding of the LRPPRC-SLIRP complex we show here that LRPPRC and SLIRP forms a hetero-dimer via interactions by polar amino acids in the RRM domain of SLIRP and three neighboring PPR motifs in the second quarter of LRPPRC, which critically contribute to the LRPPRC-SLIRP binding interface to enhance its stability. Unexpectedly, specific amino acids at this interface are located within the PPRs of LRPPRC at positions predicted to interact with RNA and within the RNP1 motif of SLIRP's RRM domain. LRPPRC binds throughout the mitochondrial transcriptome that affects its secondary structure and displays a global RNA chaperone capacity that expose single-stranded sites to ensure that RNA is accessible for its biological functions. In contrast to LRPPRC, SLIRP only weakly associates with RNA that suggests its main role is not to bind RNA, but to stabilize LRPPRC, despite being composed almost entirely of an RRM domain.