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Understanding the molecular mechanisms of organelle communication in the regulation of cellular lipid metabolism and developmental processes

Reference	BB/W015420/1
Principal Investigator / Supervisor	Professor Michael Schrader
Co-Investigators / Co-Supervisors	Dr Ruth Carmichael, Dr Steffen Scholpp
Institution	University of Exeter
Department	Biosciences
Funding type	Research
Value (£)	518,944
Status	Current
Type	Research Grant
Start date	01/10/2022
End date	30/09/2025
Duration	36 months

Abstract

Peroxisomes (PO) are multifunctional oxidative organelles that are essential for human health and development and play vital cooperative roles in lipid synthesis and breakdown. Peroxisomal lipid metabolism requires coordination with the endoplasmic reticulum (ER), mediated via membrane contacts. Previously, we discovered that these PO-ER contacts are important for inter-organelle lipid transfer for metabolism and PO biogenesis, and are mediated by the acyl-CoA binding proteins ACBD5 and ACBD4 present in the peroxisomal membrane. Recently, we revealed that one isoform of ACBD4 (ACBD4.3), which is a soluble protein, interacts with ACBD5 and localises to both PO and the nucleus. To our knowledge, this is the first protein to dually target to both PO and the nucleus, and raises an intriguing possibility of an ACBD4/5-dependent PO-ER-nucleus communication network. In this new project, we will investigate the mechanisms and functions of this novel inter-organelle regulatory network. We aim to elucidate, at the molecular and physiological level, how ACBD4 proteins orchestrate cellular lipid metabolism by regulating peroxisomal and nuclear activities in response to acyl-CoA. We will determine (1) ACBD4/5 interplay and modulation of PO-ER association using a combination of in vitro binding and mutational studies, and (2) the effects of ACBD4 proteins on nuclear function. Using genetic manipulation of mammalian cells and zebrafish embryos as well as lipid analysis, we will reveal (3) the impact of this ACBD4-regulated network on cellular lipid metabolism and, ultimately, (4) the consequences of this on development and physiology at the organismal level. This internationally collaborative project applies molecular cell biology, biochemical, transcriptomic, metabolic/lipidomic, proteomic, and in vivo approaches, as well as cutting edge imaging techniques, to improve our fundamental understanding of organelle communication and cellular lipid metabolism in health and disease.

Summary

A human cell has to carry out many complex functions to support life. To manage all these processes efficiently, cells are divided into numerous distinct compartments, known as organelles. While each type of organelle has its own specific roles, they also form part of a wider network and must communicate with each other to coordinate their functions depending on the needs of the cell. One essential function of the cell that relies on this cooperation is the production and processing of lipid molecules to 1) regulate cellular energy production; 2) break down toxic lipids to avoid their accumulation; and 3) make important building blocks for the cell, such as lipids called plasmalogens that are critically important in nerve cells. Two organelles that are vital to produce and process lipids are the endoplasmic reticulum (ER) and the peroxisome, which together form a 'metabolic hub' for these molecules. Lipids are passed between the two at sites of physical contact. Defects in these processes, caused by abnormal peroxisomes, or by the inability of the ER and peroxisomes to work together to produce the required lipids, results in severe disorders with developmental and neurological defects. In our previous work, we identified the protein components that mediate the peroxisome-ER interaction in human cells. This includes the proteins ACBD4 and ACBD5 at peroxisomes, which can both bind to lipids directly. They belong to a large family of lipid binding proteins, which are not well explored, but have recently been linked to human disease as patients with defects in these proteins have been identified. Recently, we discovered that one specific form of ACBD4, called ACBD4.3, is found in another organelle (the nucleus), but also at peroxisomes where it binds to ACBD5. The nucleus is a master regulator of cell function by responsively changing which proteins the cell produces, depending on its needs and environment. This, to our knowledge, is the first time a nuclear protein is also present at peroxisomes, indicating that there is a novel channel of communication between these two organelles that is mediated by ACBD4.3. We propose that ACBD4.3 plays important roles at both peroxisomes and the nucleus, to orchestrate cell-wide lipid metabolism. In particular, the fact that ACBD4.3 can bind to lipids raises the intriguing possibility that it may be able to relay information about the current lipid content of the cell to multiple organelles, ensuring the cell alters its lipid processing in an appropriate, coordinated fashion depending on the needs of the cell. To explore the mechanism and function of this exciting new communication link between peroxisomes, the ER and the nucleus, we will use mammalian cells to investigate 1) how ACBD4 and 5 proteins work together to control the peroxisome-ER interaction; 2) what the function of ACDB4 proteins in the nucleus is, and 3) how ACBD4 proteins impact on cellular lipid metabolism and coordinate nuclear and peroxisomal activities. Once we understand this on a cellular level, we then want to 4) investigate the consequences of this communication and regulation on the development and metabolism of a whole living system, using zebrafish as a model due to their many experimental advantages. Together, this proposal will give us crucial new insights into the fundamental regulation of cellular lipid metabolism and organelle communication networks, which could ultimately reveal new strategies to treat age-related disorders where these processes are dysregulated.

Committee	Research Committee D (Molecules, cells and industrial biotechnology)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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