Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

Abstract

Background The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. Results Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. Conclusions In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.

Naegleria’s mitotic spindles are built from unique tubulins and highlight core spindle features

“…To establish a more inclusive comparison of Naegleria α-, and β-tubulins to those of other eukaryotes, 1,191 tubulins from 200 different species were analyzed ( Table S3 ), adding sequences from Naegleria gruberi , 47 Naegleria fowleri , 77 and Acrasis kona (S. Baldauf, personal communication) to those identified as α, β, and γ tubulins using the PhyloToL pipeline. 68 Prior to alignment, sequences from the same species that were 100% identical were removed, leaving only one copy before re-merging the datasets.…”

Localization and functional characterization of the alternative oxidase in Naegleria

“…A recently published omics approach investigating the potential genes that could be driving the pathogenicity of N . fowleri demonstrated up‐regulation of mitochondrial energy conversion genes including those involved in ubiquinone biosynthesis, isocitrate dehydrogenase (TCA cycle), complex I and complex III of oxidative phosphorylation (Herman et al, 2021). While the authors have demonstrated up‐regulation of enzymes indirectly involved in oxidative stress pathway (e.g., agmatine deiminase), they were not able to demonstrate any significant change in the expression levels of any of the N .…”

Repurposing in vitro approaches for screening anti-parasitic drugs against the brain-eating amoeba Naegleria fowleri

“…Terbinafine is an antifungal drug used to treat skin infections that inhibits ergosterol synthesis by inhibiting the fungal squalene monooxygenase ( https://go.drugbank.com/drugs/DB00857 ). While these are promising candidates for the treatment of PAM (higher amoebicidal activity, improved ADMET profile and bioavailability than the reference drug amphotericin B), further multiphasic investigations combining both ‘omics ( Herman et al, 2021 ) and this newly established methods, are required to identify suitable fast-active drugs against the brain-eating amoeba.…”