Novel fungal lipid metabolism: Does the plasticity of lipid metabolism evolve to allow survival mechanisms?

Secondary Supervisor(s): Professor Dylan Owen

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Microbiology)

Project Outline

Fungal infections significantly threaten human health, particularly for immunocompromised individuals. Among various infectious fungal species, the Aspergillus genus stands out for several reasons: they are widespread fungi found in various environments, with nearly 200 species - identified, which makes exposure almost unavoidable. It causes high levels of mortality in immunocompromised patients, up to 90%. Aspergillus primarily infects through inhalation, leading to respiratory diseases that range from allergic reactions to life-threatening invasive aspergillosis. Unlike many other fungal species, it has high levels of thermotolerance and the range of temperatures they can sustain is wide (up to 50C). Finally, Aspergillus species, especially A. fumigatus, have demonstrated increasing resistance to antifungal medications like azoles, commonly used in treating fungal infections.

Here I propose to investigate the fungal biology of Aspergillus fumigatus specifically metabolic plasticity that leads to environmental and human body adaptation. We will use a comparative approach between several Aspergillus species that have different virulence or adaptability to various environmental conditions. The project will deploy interdisciplinary approach, at the first stage we will use omics (genomics and transcriptomics) to characterise Aspergillus sp in different environments. Later in the project, we will focus on specifics such as membrane biology and associated metabolism using mass spectrometry and advanced microscopy.

Objectives

• The first objective of the project focuses on investigating the lipid metabolism and membrane-associated pathways of Aspergillus species, particularly in the context of environmental resilience and virulence using an integrative omics approach (metabolomics, transcriptomics, etc.). We aim to discover how these fungi adapt to various environmental stresses, such as temperature fluctuations and hypoxic conditions, which are crucial factors in their survival, pathogenicity, and ability to evade the human immune system. By pinpointing critical metabolites and pathways, we plan to experimentally manipulate them via CRISPR/Cas genome editing to validate their role in environmental adaptability and virulence.

• If the first aim is exploratory, focusing on uncovering key pathways, the second aim will allow us to target specific mechanisms that we have found in other species. In this part of the project, we will investigate sterol and sterol surrogate synthesis in Aspergillus. From our research on Schizosaccharomyces japonicus, we found that it can use alternative biosynthesis and make hopanoids—molecules that share similar biophysical properties with sterols. This ability to synthesise hopanoids helps to resist antifungal pressure and survive in hypoxic environments. Here we will generate mutants defective in the synthesis of hopanoids and asses their environmental plasticity and ability to evade the immune response.

• Here, we will focus on how Aspergillus mutants generated in Aim 1 and Aim 2 affect:

a) the physiology of Aspergillus (its life cycle and morphology), and

b) their interactions with the innate immune system. We will establish a model using primary human lung macrophages to assess how effectively these macrophages can engulf the fungal cells. We will focus on the membrane biology of this process and the biophysical properties of the membranes of both pathogen and host cells.

The methods that will be used throughout the PhD are diverse and interdisciplinary:

The first and second aims will rely on molecular biology techniques, including genetic manipulation using CRISPR/Cas. You will also gain experience in generating and analyzing multiomics data, integrating metabolomics and transcriptomics to identify pathways responsible for specific phenotypes. Aims 2 and 3 will involve advanced imaging and biophysical characterization of membrane properties.