Genome-wide comparative analysis of conserved genes and associated pathways in pathogenic Amoebae

• Main Author: Goh, Tiong Keat
• Format: Thesis
• Published: 2020
• Subjects: QR Microbiology
• Online Access: http://eprints.sunway.edu.my/2420/

Pathogenic amoebae are ubiquitous and are capable of causing serious eye, brain and intestinal infections in humans. Having the ability to harbour other microbes, these amoebae can further posit health concerns by aiding in disease transmission. Despite decades of research, these amoebae remain incompletely understood and management of their infection remains unsatisfactory. This situation warrants for the search of better understanding and therapeutics in handling these amoebae infections. Available genome and transcriptome of Acanthamoeba castellanii, Balamuthia mandrillaris, Naegleria fowleri, Entamoeba dispar and Entamoeba histolytica were retrieved for identifying putative genes. Briefly, they were used for determining open reading frames and subsequently annotated using BlastKOALA. The obtained dataset was then managed, compared and analysed for insights. Protein-modelling and function prediction were also carried out for selected genes of interest. Furthermore, several non-human related genes were also selected for validation and characterization through anti-amoebic assays. In the present study, 594 genes that are conserved across all five amoebae were identified, while pathways relating to cell cycle, apoptosis, calcium signaling, starch and sucrose metabolism, steroid biosynthesis and amoebiasis have been suggested for future investigations. Most notably, 8 genes were determined to be present across all four pathogenic amoebae (PSMB7, K07023, TWF, SYVN1, COPS2, DIM1, MAK16, DCUN1D4_5) while being absent in the non-pathogenic E. dispar, hinting at their potential of being pathogenicity factors. Protein structures and functions of highlighted genes were also predicted for further clarity. Additionally, the presence and expression of NOP6 gene that is specific to A. castellanii were also proven, but its underlying function remains elusive. In summary, gene repertoires of these amoebae were determined, while interesting gene candidates have been proposed for future studies with accompanying structural and functional predictions. This new-found information is aimed to help improve the current understanding of these amoebae and to contribute in future development of novel therapeutics for combating amoebae infections.