Mass Spectrometry-Based Proteomics of Fungal Pathogenesis, Host-Fungal Interactions, and Antifungal Development

Abstract

The prevalence of fungal diseases is increasing on a global scale, ranging from acute to systemic infections caused by commensal or pathogenic microorganisms, often associated with the immune status of the host. Morbidity and mortality rates remain high and our ability to treat fungal infections is challenged by a limited arsenal of antifungal agents and the emergence of drug resistant pathogens. There is a high demand for new approaches to elucidate the fungal mechanisms of pathogenesis and the interplay between host and pathogen to discover novel treatment options. Moreover, the need for improved drug efficacy and reduced host toxicity requires the identification and characterization of antifungal biological targets and molecular mechanisms of action. Mass spectrometry (MS)-based proteomics is a rapidly advancing field capable of addressing these priorities by providing comprehensive information on the dynamics of cellular processes, modifications, and interactions. In this Review, we focus on applications of MS-based proteomics in a diverse array of fungal pathogens and host systems to define and distinguish the molecular details of fungal pathogenesis and host-fungal interactions. We also explore the emerging role of MS-based proteomics in the discovery and development of novel antifungal therapies and provide insight into the future of MS-based proteomics in fungal biology.

Keywords: antifungals; fungal pathogenesis; host–pathogen interactions; mass spectrometry-based proteomics.

Figure 1

Publications from 2000–2017 of proteomic applications in fungal biology. An in-house developed R-script was used to search PubMed for publications using the following search terms within the abstract and/or title: (i) “fungal OR fungi AND proteomics NOT host”; (ii) “host–fungal interactions OR host–fungi interactions AND proteomics”; and (iii) “antifungal AND proteomics”. Note: y-axis plotted on log₁₀ scale for improved data visualization.

Figure 2

Graphical representation of MS-based proteomics workflows. Top-down proteomics analyzes intact proteins by LC–MS/MS for the identification and quantification of unique proteoforms following separation of proteins by size and peak isolation. Bottom-up proteomics measures proteolytic digested proteins (peptides) by LC–MS/MS for unbiased identification and quantification of proteins within a sample. Targeted proteomics measures a pre-defined set of peptides (isolation of parent ion by mass in Q1, collision of the ion Q2, and mass filtering of product ion in Q3) by LC–MS/MS for identification, characterization, and quantification of specific proteins and biomarkers. Figure generated using BioRender.com.

Figure 3

Quantitative proteomics of distinct fungal systems. (A) The cellular compartment for total proteome profiling encompasses organelles, the cell wall, intracellular proteins, and polysaccharide capsule as demonstrated in C. neoformans. (B) The extracellular environment for secretome profiling includes secreted proteins and peptides, as well as vesicles actively or passively released by the cell. (C) Survival states include the production of spores or desiccated yeast cells and the formation of biofilms. Figures not drawn to scale; generated using BioRender.com.