Description of Virulent Factors and Horizontal Gene Transfers of Keratitis-Associated Amoeba Acanthamoeba Triangularis by Genome Analysis

Abstract

Acanthamoeba triangularis strain SH 621 is a free-living amoeba belonging to Acanthamoeba ribo-genotype T4. This ubiquitous protist is among the free-living amoebas responsible for Acanthamoeba keratitis, a severe infection of human cornea. Genome sequencing and genomic comparison were carried out to explore the biological functions and to better understand the virulence mechanism related to the pathogenicity of Acanthamoeba keratitis. The genome assembly harbored a length of 66.43 Mb encompassing 13,849 scaffolds. The analysis of predicted proteins reported the presence of 37,062 ORFs. A complete annotation revealed 33,168 and 16,605 genes that matched with NCBI non-redundant protein sequence (nr) and Cluster of Orthologous Group of proteins (COG) databases, respectively. The Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) annotation reported a great number of genes related to carbohydrate, amino acid and lipid metabolic pathways. The pangenome performed with 8 available amoeba genomes belonging to genus Acanthamoeba revealed a core genome containing 843 clusters of orthologous genes with a ratio core genome/pangenome of less than 0.02. We detected 48 genes related to virulent factors of Acanthamoeba keratitis. Best hit analyses in nr database identified 99 homologous genes shared with amoeba-resisting microorganisms. This study allows the deciphering the genome of a free-living amoeba with medical interest and provides genomic data to better understand virulence-related Acanthamoeba keratitis.

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

“…Similarly to A. polyphaga , most of these genes belong to Pandoravirus species ( P. quercus , P. inopinatum , P. macleodensis , P. neocaledonia , and P. salinus ). Additionally, homologs of Medusavirus , Mimivirus , Tupanvirus , Catovirus , Marseillevirus , Pithovirus sibericum , and Mollivirus sibericum were identified as part of the genomic structure of A. triangularis [ 32 ]. This extends considerably the repertoire of genes that Acanthamoeba species can integrate into their genome.…”

“…From this set of bacterial genes, 44 presented homology with Chlamydia spp., 16 with Acinetobacter spp. and Pseudomonas spp., and about two hypothetic proteins were related to Legionella pneumophila , all microorganisms known for their pathogenic capacity in humans [ 32 ]. It is possible that the great capacity of Acanthamoeba spp.…”

“…Finally, Hasni et al [ 32 ] identified virulence factors related to pathogenicity through a comparative genomics approach, comparing Acanthamoeba species such as A. triangularis , A. castellanii with other FLA ( N. fowleri , N. gruberi , N. lovaniensis , E. histolytica , D. discoideum , and W. magna ). This analysis reported 1004 orthologs within the Acanthamoeba genus.…”

“…These virulence factors are common ground with other pathogenic FLA, the mannose-binding protein used by the amoeba to mediate the adhesion with the host epithelial cells, proteases utilized for host evasion, and phospholipases for cell disruption and lysis as well as induction of inflammatory response. In the case of indirect virulence factors, the study mainly reported genes that code for heat shock proteins, vital for the survival of the pathogenic amoeba during infection [ 32 ].…”

Proteomics and Lipidomics Investigations to Decipher the Behavior of Willaertia magna C2c Maky According to Different Culture Modes

“…However, these methods have not yet been widely applied to study FLAs. Indeed, only a few studies based on genomics, transcriptomics and proteomics are described in the literature [ 8 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ].…”