Avirulent UG10 Entamoeba histolytica mutant derived from HM-1:IMSS strain shows limited genome variability and aberrant 5-methyl cytosine genomic distribution

• Published in: Molecular and biochemical parasitology 2024-12, Vol.260, p.111647, Article 111647
• Main Authors: Vargas-Maya, Naurú Idalia, Maunakea, Alika K., Ramírez-Montiel, Fátima Berenice, Sultana, Razvan, Peres, Rafael, Macías-Cervantes, Quetzalli Xiadany, Medina-Nieto, Ana Laura, Rangel-Serrano, Ángeles, Martínez-Álvarez, José A., Páramo-Pérez, Itzel, Anaya-Velázquez, Fernando, Padilla-Vaca, Felipe, Franco, Bernardo
• Format: Article
• Language: English
• Subjects: DNA Methylation; Entamoeba histolytica; Entamoeba histolytica - genetics; Entamoeba histolytica - metabolism; Entamoeba histolytica - pathogenicity; Genetic Variation; Genome, Protozoan; MeDIP-seq; Mutation; Protozoan Proteins - genetics; Protozoan Proteins - metabolism; UG10 strain; Virulence - genetics; Virulence determinants; Virulence factors; Virulence Factors - genetics; Virulence Factors - metabolism; Whole Genome Sequencing
• ISSN: 0166-6851; 1872-9428; 1872-9428
• DOI: 10.1016/j.molbiopara.2024.111647

Entamoeba histolytica, an intestinal parasite of global significance, poses substantial health risks with its associated high morbidity and mortality rates. Despite the current repertoire of molecular tools for the study of gene function in, the regulatory mechanisms governing its pathogenicity remain largely unexplored. This knowledge gap underscores the need to elucidate key genetic determinants orchestrating cellular functions critical to its virulence. Previously, our group generated an avirulent strain, termed UG10, with the same genetic background as the HM1:IMSS strain. UG10 strain, despite showing normal expression levels of well-known virulence factors, was unable to perform in-vitro and in-vivo activities related to amoebic virulence. In this study, we aimed to uncover the genome-wide modifications that rendered the avirulent phenotype of the UG10 strain through whole-genome sequencing. As a complementary approach, we conducted Methylated DNA Immunoprecipitation coupled with sequencing (MeDIP-seq) analysis on both the highly virulent HM1:IMSS strain and the low-virulence UG10 strain to uncover the genome-wide methylation profile. These dual methodologies revealed two aspects of the UG10 avirulent strain. One is the random integration of fragments from the ribosomal gene cluster and tRNA genes, ranging from 120 to 400 bp; and secondly, a clear, enriched methylation profile in the coding and non-coding strand relative to the start codon sequence in genes encoding small GTPases, which is associated with the previously described avirulent phenotype. This study provides the foundation to explore other genetic and epigenetic regulatory circuitries in E. histolytica and novel targets to understand the pathogenic mechanism of this parasite. •Entamoeba histolytica has a genomic structure highly variable.•Using strains with different virulence phenotype can uncover virulence mechanisms.•UG10 strain exhibits low virulence phenotype in comparison with HM1:IMSS strain.•Whole genome sequence of UG10 strain revealed discreate modifications.•MeDIP-seq analysis revealed a differentially methylated upstream regions.