Periodic Reporting for period 5 - Chap4Resp (Catching in action a novel bacterial chaperone for respiratory complexes)
Periodo di rendicontazione: 2021-10-01 al 2022-03-31
The first and the largest enzyme of the respiratory chain is Complex I (CI), which core is highly conserved from bacteria to humans. This project focused on the structure-function relationships of a three-component protein system proposed to be involved in CI assembly is enterobacteria. In parallel, as a part of a larger collaborative effort, the structure and function of the mitochondrial CI assembly (MCIA) complex was addressed. The project overturned the previous view on the bacterial LdcI-RavA-ViaA triad and resulted in novel models of its mechanism of action, setting the stage for future investigations of an unprecedented molecular network that links the triad with bacterial stress adaptation, membrane homeostasis, respiratory complexes and aminoglycoside bactericidal activity. In addition, we provided a structural basis for the MCIA complex architecture and suggested a novel mechanism for coordinating the regulation of the mitochondrial energetic pathways, with implications on the molecular etiology of the Alzheimer’s disease.
Our findings led us to propose that RavA and ViaA chaperone certain respiratory complexes indirectly, by acting on lipid microdomains in which these complexes are inserted. This hypothesis aligns with our observations on the in cellulo distribution of LdcI. In addition to opening exciting research directions on the links between the LdcI-RavA-ViaA triad and bacterial stress adaptation, respiration, membrane homeostasis and aminoglycoside bactericidal activity, these results improve our knowledge of enterobacterial pathways mobilised in response to AGs under anaerobiosis. Considering that AG efficiency is dramatically reduced in anaerobic conditions encountered by enteric pathogens inside their human host, elucidation of mechanisms allowing for the usage of decreased dosage and consequently lesser toxicity may lead to safer use of this family of antibiotics against a wider range of infections.
Because the direct interaction between the LdcI-RavA-ViaA triad and respiratory complexes could not be confirmed, we decided to extend our work to the MCIA complex, proposed to be functionally analogous to the LdcI-RavA-ViaA triad but undoubtedly binding mitochondrial Complex I. We solved the structures of one isolated protein of the MCIA complex and of its binary subcomplex with another MCIA partner, and revealed a novel mechanism of regulation, crucial for efficient energy production in mitochondria. This set us on track for elucidating the role played by the MCIA complex in CI assembly with a goal to shed light on the mitochondrial bioenergetic pathways and their role in physiology and pathology, particularly in Alzheimer’s disease.
Finally, the project contained sections on methodological development for cryo-ET that we initially planned to use for identification of the LdcI-RavA cage inside E. coli minicells. While we successfully designed and characterised a minicell-producing strain suitable for cryo-ET, the LdcI-RavA complex partitioned uniquely in the mother cells. Thus, instead of the LdcI-RavA complex, we benchmarked the minicells and our cryo-ET image analysis tools that offer streamlined interaction between state-of-the-art software packages, by solving the structure of the core signalling unit of the E. coli chemosensory array. In addition, we showed that our cryo-ET image analysis framework can successfully result in an atomic resolution structure solved from a publicly available dataset ( EMPIAR-10164) commonly used for benchmarking. We created a comprehensive step-by-step guide to obtaining this structure and offered it on a collaborative, online ressource https://teamtomo.org/ that we established as a platform for sharing knowledge about cryo-ET data processing. This platform is now widely used and other researchers contribute their expertise for the common benefit of the growing cryo-ET community.