Luis Daniel Cruz Zaragoza

Research Interests

• Protein-driven biogenesis and identity of mitochondria and peroxisomes
• Mechanisms of mitochondrial protein import and the translocation/insertion machinery, the TOM, TIM23 and TIM22 complexes and the OXA insertase, together with ATP-driven chaperones such as mtHsp70/HSPA9
• Co-translational coupling of mitochondrial translation to membrane-protein insertion, and the quality-control networks that surveil it
• Protein machinery of inter-organelle membrane contact sites, with particular emphasis on peroxisome-mitochondria contacts (PerMit): tethering complexes, redox coordination, and metabolite channeling
• Post-transcriptional control of organelle proteostasis by RNA-binding proteins (e.g. the IGF2BP family), how cytosolic factors govern the localization, translation and stability of organelle-targeted transcripts
• Organelle dysfunction as a driver of disease: mitochondrial disorders (MELAS/MERRF), neurodegeneration, and cancer-cell metabolic reprogramming through the LRH-1/NR5A2 nuclear receptor
• Protein engineering and synthetic cell biology: fluorescent biosensors and chemically inducible systems to control protein localization and activity in living cells with high temporal precision

Current Research Projects

• Protein architecture of peroxisome-mitochondria contact sites (PerMit). Mapping the tethering complexes, regulatory hubs and signaling intermediates that physically and functionally connect the two organelles, and defining how these contacts coordinate redox balance and metabolite exchange under stress (supported by an NSERC Discovery Grant).
• Programmable control of mitochondrial gene expression in living cells. Building on the peptide-morpholino chimera platform (Science, 2025) to silence or titrate the synthesis of individual mitochondrial-encoded OXPHOS proteins in intact cells, a tool to dissect assembly, quality control, and the bioenergetic consequences of selective protein loss.
• Modeling mitochondrial translation disorders. Using titratable depletion approaches to recreate the protein-synthesis defects underlying mitochondrial disease (MELAS/MERRF and related mt-tRNA disorders) and to follow how impaired mitochondrial translation propagates to OXPHOS protein assembly and cellular metabolism.
• LRH-1/NR5A2 as a metabolic regulator in triple-negative breast cancer. Investigating how this nuclear receptor reprograms cancer-cell energy metabolism, integrating pharmacology with bioenergetic profiling.
• Quantitative tools for mitochondrial protein import and metabolism.

Tools and Expertises

• Mitochondrial and organelle biochemistry: isolation of functional mitochondria; in vitro and in organello import and translation assays; BN-/SDS-PAGE and complexome analysis; subcellular fractionation.
• Targeted manipulation of organelle gene expression: peptide-morpholino chimera technology to silence and titrate mitochondrial protein synthesis in living cells (flagship method; Cell, 2021 and Science, 2025).
• Interactome and contact-site mapping: proximity-dependent biotinylation (TurboID, APEX2) coupled to quantitative mass-spectrometry proteomics; protein-protein interaction analysis; interpretation of structural proteomics.
• Imaging and protein-activity tools: quantitative and live-cell fluorescence microscopy; fluorescence-based protein-import assays; design of fluorescent biosensors and chemically inducible systems for spatiotemporal control of protein localization and activity.
• Cellular bioenergetics: Seahorse XF Pro extracellular-flux respirometry, linking protein function to metabolic phenotype.
• Model systems: mammalian cell culture, Saccharomyces cerevisiae genetics, and patient-derived cells, with iPSC models accessed through collaboration.
• RNA-based tools: design of antisense and RNA reagents (and, with collaborators, mRNA/saRNA–LNP approaches) to modulate protein expression.