The transcriptome ofBalamuthia mandrillaristrophozoites for structure-based drug design

Abstract

<jats:title>Abstract</jats:title><jats:p><jats:italic>Balamuthia mandrillaris</jats:italic>, a pathogenic free-living amoeba (FLA), causes cutaneous skin lesions as well as the brain-eating disease: <jats:italic>Balamuthia</jats:italic> granulomatous amoebic encephalitis (GAE). These diseases, and diseases caused by other pathogenic FLA, <jats:italic>Naegleria fowleri</jats:italic> or <jats:italic>Acanthamoeba</jats:italic> species, are minimally studied from a drug discovery perspective; few targets have been validated or characterized at the molecular level, and little is known about the biochemical pathways necessary for parasite survival. Chemotherapies for CNS disease caused by <jats:italic>B. mandrillaris</jats:italic> require vast improvement. Current therapeutics are limited to a small number of drugs that were previously discovered in the last century through <jats:italic>in vitro</jats:italic> testing or identified after use in the small pool of surviving reports.</jats:p><jats:p>Using our recently published methodology to identify potentially useful therapeutics, we screened a collection of 85 compounds that have previously been reported to have antiparasitic activity. We identified 59 compounds that impacted growth at concentrations below 220 μM. Since there is no fully annotated genome or proteome, we used RNA-Seq to reconstruct the transcriptome of <jats:italic>B. mandrillaris</jats:italic> and locate the coding sequences of the specific genes potentially targeted by the compounds identified to inhibit trophozoite growth. We determined the sequence of 17 of these target genes and obtained expression clones for 15 that we validated by direct sequencing.</jats:p>

Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants

“…EvidentialGene use for gene set reconstruction is increasing in biomedical genomics including human disease studies. A recent human disease study of a pathogenic amoeba (Phan et al 2020) with Evigene led to discovery of therapeutic compounds targeting amoeba genes. A USDA resource for pig genes, relevant to agricultural and biomedical uses, benefits from Evigene (Dawson et al 2020).…”

Application of the omics sciences to the study of Naegleria fowleri, Acanthamoeba spp., and Balamuthia mandrillaris: current status and future projections

“…A recent application of functional genomics performed by Phan et al [ 63 ] obtained the first transcriptome of B. mandrillaris (strain V039) to reconstruct the proteome and identify the genes susceptible to 85 compounds with antimicrobial activity against this amoeba. From the de novo assembly, they found a higher percentage of similarity with A. castellanii str.…”

“…Neff (45%) previously reported by Greninger et al [ 29 ] when analyzing the mitochondrial genomes of B. mandrillaris . Additionally, it should be noted that with the transcriptome, supported by the draft genome of strain V039 deposited in GenBank, functional annotation of 80% of the proteins of this amoeba was done [ 63 ], finding 15 candidate proteins to be the target of drugs to fight infections like GAE. These proteins include mainly S-adenosyl-L-homocysteine-hydrolase, Histone deacetylase 1, HSP90-alpha, Exportin-1, and some copies of DNA topoisomerase II.…”